Yannis Schumann
| Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 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 2024-07-24 11:39 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 157/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| 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 | | ||||||||
|
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: 2024-07-23 22:13:27 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 22:15:44 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 137.8 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 8.55 0.5 18.5
* 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")
2024-07-23 22:14:29.824724 INFO::Formatting Data.
2024-07-23 22:14:29.827867 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:29.842518 INFO::Removing potential empty rows and columns
2024-07-23 22:14:30.164393 INFO::Found 0 missing values.
2024-07-23 22:14:30.169526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:30.170917 INFO::Done
2024-07-23 22:14:30.172179 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:30.191892 INFO::Starting hierarchical adjustment
2024-07-23 22:14:30.19361 INFO::Found 3 batches.
2024-07-23 22:14:30.1949 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:30.196923 INFO::Using default BPPARAM
2024-07-23 22:14:30.198147 INFO::Processing subtree level 1
2024-07-23 22:14:32.773293 INFO::Adjusting the last 1 batches sequentially
2024-07-23 22:14:32.775574 INFO::Done
2024-07-23 22:14:32.776856 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:32.779768 INFO::ASW Batch was -0.108369061052682 prior to batch effect correction and is now -0.108369061052682 .
2024-07-23 22:14:32.781313 INFO::Total function execution time is 2.95734310150146 s and adjustment time is 2.58224296569824 s ( 87.32 )
2024-07-23 22:14:32.802761 INFO::Formatting Data.
2024-07-23 22:14:32.804399 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:32.806263 INFO::Removing potential empty rows and columns
2024-07-23 22:14:32.808235 INFO::Found 0 missing values.
2024-07-23 22:14:32.809918 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.
2024-07-23 22:14:32.822647 INFO::Formatting Data.
2024-07-23 22:14:32.823602 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:32.824676 INFO::Removing potential empty rows and columns
2024-07-23 22:14:32.825839 INFO::Found 0 missing values.
2024-07-23 22:14:32.827429 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.
2024-07-23 22:14:32.843908 INFO::Formatting Data.
2024-07-23 22:14:32.844981 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:32.846096 INFO::Removing potential empty rows and columns
2024-07-23 22:14:32.847239 INFO::Found 0 missing values.
2024-07-23 22:14:32.848317 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.
2024-07-23 22:14:32.852196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:32.852986 INFO::Done
2024-07-23 22:14:32.853751 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:32.855803 INFO::Starting hierarchical adjustment
2024-07-23 22:14:32.856691 INFO::Found 2 batches.
2024-07-23 22:14:32.857558 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:32.858358 INFO::Using default BPPARAM
2024-07-23 22:14:32.859057 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:14:32.860243 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:14:32.877323 INFO::Done
2024-07-23 22:14:32.878195 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:32.880257 INFO::ASW Batch was -0.0462043872877273 prior to batch effect correction and is now -0.115496874481558 .
2024-07-23 22:14:32.881217 INFO::Total function execution time is 0.0374069213867188 s and adjustment time is 0.0207350254058838 s ( 55.43 )
2024-07-23 22:14:32.88397 INFO::Formatting Data.
2024-07-23 22:14:32.884794 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:32.891518 INFO::Formatting Data.
2024-07-23 22:14:32.892363 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:32.893375 INFO::Removing potential empty rows and columns
2024-07-23 22:14:32.894524 INFO::Found 0 missing values.
2024-07-23 22:14:32.897144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:32.897862 INFO::Done
2024-07-23 22:14:32.898551 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:32.900704 INFO::Starting hierarchical adjustment
2024-07-23 22:14:32.901617 INFO::Found 2 batches.
2024-07-23 22:14:32.902369 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:32.90314 INFO::Using default BPPARAM
2024-07-23 22:14:32.903833 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:14:32.904883 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:14:32.917336 INFO::Done
2024-07-23 22:14:32.918215 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:32.920319 INFO::ASW Batch was 0.0315590947226101 prior to batch effect correction and is now -0.0588290851594021 .
2024-07-23 22:14:32.921279 INFO::Total function execution time is 0.0297880172729492 s and adjustment time is 0.0158259868621826 s ( 53.13 )
2024-07-23 22:14:32.922442 INFO::Formatting Data.
2024-07-23 22:14:32.923222 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:32.924218 INFO::Removing potential empty rows and columns
2024-07-23 22:14:32.925325 INFO::Found 0 missing values.
2024-07-23 22:14:32.927766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:32.928473 INFO::Done
2024-07-23 22:14:32.929163 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:32.931204 INFO::Starting hierarchical adjustment
2024-07-23 22:14:32.932058 INFO::Found 2 batches.
2024-07-23 22:14:32.932753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:32.933528 INFO::Using default BPPARAM
2024-07-23 22:14:32.934229 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:14:32.935284 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:14:32.947049 INFO::Done
2024-07-23 22:14:32.947856 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:32.949908 INFO::ASW Batch was 0.0315590947226101 prior to batch effect correction and is now -0.0588290851594021 .
2024-07-23 22:14:32.950855 INFO::Total function execution time is 0.0284039974212646 s and adjustment time is 0.0151150226593018 s ( 53.21 )
2024-07-23 22:14:36.19599 INFO::Formatting Data.
2024-07-23 22:14:36.197391 INFO::Recognized SummarizedExperiment
2024-07-23 22:14:36.19855 INFO::Typecasting input to dataframe.
2024-07-23 22:14:36.244497 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:36.246773 INFO::Removing potential empty rows and columns
2024-07-23 22:14:36.252192 INFO::Found 0 missing values.
2024-07-23 22:14:36.262065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:36.263609 INFO::Done
2024-07-23 22:14:36.264938 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:36.271335 INFO::Starting hierarchical adjustment
2024-07-23 22:14:36.272897 INFO::Found 2 batches.
2024-07-23 22:14:36.274165 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:36.276123 INFO::Using default BPPARAM
2024-07-23 22:14:36.277313 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:14:36.279245 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:14:36.357826 INFO::Done
2024-07-23 22:14:36.359293 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:36.365799 INFO::ASW Batch was -0.00648648821376381 prior to batch effect correction and is now -0.0951341733182387 .
2024-07-23 22:14:36.367541 INFO::Total function execution time is 0.171963930130005 s and adjustment time is 0.0851700305938721 s ( 49.53 )
2024-07-23 22:14:36.398287 INFO::Formatting Data.
2024-07-23 22:14:36.399878 INFO::Recognized SummarizedExperiment
2024-07-23 22:14:36.40136 INFO::Typecasting input to dataframe.
2024-07-23 22:14:36.417057 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:36.419413 INFO::Removing potential empty rows and columns
2024-07-23 22:14:36.425755 INFO::Found 0 missing values.
2024-07-23 22:14:36.437669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:36.439142 INFO::Done
2024-07-23 22:14:36.440497 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:36.447535 INFO::Starting hierarchical adjustment
2024-07-23 22:14:36.449188 INFO::Found 2 batches.
2024-07-23 22:14:36.450485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:36.451924 INFO::Using default BPPARAM
2024-07-23 22:14:36.453186 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:14:36.455313 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:14:36.496824 INFO::Done
2024-07-23 22:14:36.498342 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:36.505451 INFO::ASW Batch was -0.0112424022708995 prior to batch effect correction and is now -0.0112424022708995 .
2024-07-23 22:14:36.507287 INFO::Total function execution time is 0.108954191207886 s and adjustment time is 0.0478761196136475 s ( 43.94 )
2024-07-23 22:14:36.543174 INFO::Formatting Data.
2024-07-23 22:14:36.544895 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:36.54688 INFO::Removing potential empty rows and columns
2024-07-23 22:14:36.548995 INFO::Found 0 missing values.
2024-07-23 22:14:36.554153 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:36.555469 INFO::Done
2024-07-23 22:14:36.556734 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:36.560319 INFO::Starting hierarchical adjustment
2024-07-23 22:14:36.561836 INFO::Found 3 batches.
2024-07-23 22:14:36.563107 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:36.564529 INFO::Using default BPPARAM
2024-07-23 22:14:36.56577 INFO::Processing subtree level 1
2024-07-23 22:14:46.372761 INFO::Adjusting the last 1 batches sequentially
2024-07-23 22:14:46.374742 INFO::Done
2024-07-23 22:14:46.375584 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:46.377866 INFO::ASW Batch was -0.0627473492318455 prior to batch effect correction and is now -0.159751985030295 .
2024-07-23 22:14:46.378839 INFO::Total function execution time is 9.83590006828308 s and adjustment time is 9.81317210197449 s ( 99.77 )
2024-07-23 22:14:46.399181 INFO::Skipping initial DF formatting
2024-07-23 22:14:46.400561 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:46.407419 INFO::Starting hierarchical adjustment
2024-07-23 22:14:46.409055 INFO::Found 5 batches.
2024-07-23 22:14:46.410375 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:46.411725 INFO::Using default BPPARAM
2024-07-23 22:14:46.412957 INFO::Processing subtree level 1
2024-07-23 22:14:49.422418 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:14:49.424532 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:14:49.447534 INFO::Done
2024-07-23 22:14:49.448927 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:49.453834 INFO::ASW Batch was 0.544381970687782 prior to batch effect correction and is now 0.544381970687782 .
2024-07-23 22:14:49.455053 INFO::ASW Label was 0.351199464246238 prior to batch effect correction and is now 0.351199464246238 .
2024-07-23 22:14:49.456429 INFO::Total function execution time is 3.05737400054932 s and adjustment time is 3.03871011734009 s ( 99.39 )
2024-07-23 22:14:49.478749 INFO::Formatting Data.
2024-07-23 22:14:49.479738 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:49.480905 INFO::Removing potential empty rows and columns
2024-07-23 22:14:49.482007 INFO::Found 0 missing values.
2024-07-23 22:14:49.485466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:49.486184 INFO::Done
2024-07-23 22:14:49.486875 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:49.489835 INFO::Starting hierarchical adjustment
2024-07-23 22:14:49.490704 INFO::Found 5 batches.
2024-07-23 22:14:49.4914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:49.492187 INFO::Using default BPPARAM
2024-07-23 22:14:49.493028 INFO::Processing subtree level 1
2024-07-23 22:14:52.516526 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:14:52.518568 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:14:52.537523 INFO::Done
2024-07-23 22:14:52.538883 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:52.543526 INFO::ASW Batch was 0.380066939101517 prior to batch effect correction and is now 0.0198231658044279 .
2024-07-23 22:14:52.544823 INFO::ASW Label was 0.32468344257437 prior to batch effect correction and is now 0.812920307712894 .
2024-07-23 22:14:52.546334 INFO::Total function execution time is 3.06758689880371 s and adjustment time is 3.04686498641968 s ( 99.32 )
2024-07-23 22:14:52.547842 INFO::Formatting Data.
2024-07-23 22:14:52.549173 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:52.550799 INFO::Removing potential empty rows and columns
2024-07-23 22:14:52.552525 INFO::Found 0 missing values.
2024-07-23 22:14:52.558262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:52.559458 INFO::Done
2024-07-23 22:14:52.560595 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:52.565072 INFO::Starting hierarchical adjustment
2024-07-23 22:14:52.566436 INFO::Found 5 batches.
2024-07-23 22:14:52.567544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:52.568768 INFO::Using default BPPARAM
2024-07-23 22:14:52.569881 INFO::Processing subtree level 1
2024-07-23 22:14:55.503631 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:14:55.505773 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:14:55.524588 INFO::Done
2024-07-23 22:14:55.526008 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:55.529571 INFO::ASW Batch was 0.380066939101517 prior to batch effect correction and is now 0.0198231658044279 .
2024-07-23 22:14:55.530392 INFO::ASW Label was 0.32468344257437 prior to batch effect correction and is now 0.812920307712894 .
2024-07-23 22:14:55.531351 INFO::Total function execution time is 2.98360013961792 s and adjustment time is 2.95831704139709 s ( 99.15 )
2024-07-23 22:14:55.549484 INFO::Formatting Data.
2024-07-23 22:14:55.550548 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:55.551755 INFO::Removing potential empty rows and columns
2024-07-23 22:14:55.553512 INFO::Found 0 missing values.
2024-07-23 22:14:55.559258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:55.560593 INFO::Done
2024-07-23 22:14:55.561854 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:55.566661 INFO::Starting hierarchical adjustment
2024-07-23 22:14:55.568147 INFO::Found 5 batches.
2024-07-23 22:14:55.569364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:55.57065 INFO::Using default BPPARAM
2024-07-23 22:14:55.571671 INFO::Processing subtree level 1
2024-07-23 22:14:58.61423 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:14:58.616314 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:14:58.633067 INFO::Done
2024-07-23 22:14:58.634361 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:14:58.638616 INFO::ASW Batch was 0.682987793851538 prior to batch effect correction and is now -0.102693558107826 .
2024-07-23 22:14:58.639459 INFO::ASW Label was 0.0679460523403777 prior to batch effect correction and is now 0.813907808747184 .
2024-07-23 22:14:58.640418 INFO::Total function execution time is 3.0910530090332 s and adjustment time is 3.06512689590454 s ( 99.16 )
2024-07-23 22:14:58.641348 INFO::Formatting Data.
2024-07-23 22:14:58.642135 INFO::Replacing NaNs with NAs.
2024-07-23 22:14:58.643154 INFO::Removing potential empty rows and columns
2024-07-23 22:14:58.644226 INFO::Found 0 missing values.
2024-07-23 22:14:58.647688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:14:58.648666 INFO::Done
2024-07-23 22:14:58.649849 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:14:58.654198 INFO::Starting hierarchical adjustment
2024-07-23 22:14:58.655567 INFO::Found 5 batches.
2024-07-23 22:14:58.656637 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:14:58.657816 INFO::Using default BPPARAM
2024-07-23 22:14:58.658874 INFO::Processing subtree level 1
2024-07-23 22:15:01.628907 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:15:01.630931 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:15:01.648935 INFO::Done
2024-07-23 22:15:01.650285 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:01.654673 INFO::ASW Batch was 0.682987793851538 prior to batch effect correction and is now -0.102693558107826 .
2024-07-23 22:15:01.655925 INFO::ASW Label was 0.0679460523403777 prior to batch effect correction and is now 0.813907808747184 .
2024-07-23 22:15:01.657413 INFO::Total function execution time is 3.0160071849823 s and adjustment time is 2.99353313446045 s ( 99.25 )
2024-07-23 22:15:01.680002 INFO::Formatting Data.
2024-07-23 22:15:01.681488 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:01.683178 INFO::Removing potential empty rows and columns
2024-07-23 22:15:01.684913 INFO::Found 0 missing values.
2024-07-23 22:15:01.688762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:01.689947 INFO::Done
2024-07-23 22:15:01.691119 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:01.695586 INFO::Starting hierarchical adjustment
2024-07-23 22:15:01.697009 INFO::Found 2 batches.
2024-07-23 22:15:01.69819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:15:01.699467 INFO::Using default BPPARAM
2024-07-23 22:15:01.700664 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:15:01.702363 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:15:01.72121 INFO::Done
2024-07-23 22:15:01.722547 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:01.726929 INFO::ASW Batch was 0.462180864598136 prior to batch effect correction and is now 0.039210317365227 .
2024-07-23 22:15:01.728126 INFO::ASW Label was 0.641072202308414 prior to batch effect correction and is now 0.910466542824206 .
2024-07-23 22:15:01.729561 INFO::Total function execution time is 0.0496740341186523 s and adjustment time is 0.024360179901123 s ( 49.04 )
2024-07-23 22:15:01.730986 INFO::Formatting Data.
2024-07-23 22:15:01.732229 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:01.733766 INFO::Removing potential empty rows and columns
2024-07-23 22:15:01.735422 INFO::Found 0 missing values.
2024-07-23 22:15:01.739188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:01.740316 INFO::Done
2024-07-23 22:15:01.741444 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:01.746009 INFO::Starting hierarchical adjustment
2024-07-23 22:15:01.747411 INFO::Found 2 batches.
2024-07-23 22:15:01.748516 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:15:01.749701 INFO::Using default BPPARAM
2024-07-23 22:15:01.750794 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:15:01.752388 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:15:01.771161 INFO::Done
2024-07-23 22:15:01.772527 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:01.777172 INFO::ASW Batch was 0.462180864598136 prior to batch effect correction and is now 0.039210317365227 .
2024-07-23 22:15:01.778493 INFO::ASW Label was 0.641072202308414 prior to batch effect correction and is now 0.910466542824206 .
2024-07-23 22:15:01.780031 INFO::Total function execution time is 0.0490310192108154 s and adjustment time is 0.0239100456237793 s ( 48.77 )
2024-07-23 22:15:01.800811 INFO::Formatting Data.
2024-07-23 22:15:01.80224 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:01.803847 INFO::Removing potential empty rows and columns
2024-07-23 22:15:01.805434 INFO::Found 0 missing values.
2024-07-23 22:15:01.808575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:01.809666 INFO::Done
2024-07-23 22:15:01.810767 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:01.81369 INFO::Starting hierarchical adjustment
2024-07-23 22:15:01.814994 INFO::Found 2 batches.
2024-07-23 22:15:01.816083 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:15:01.817282 INFO::Using default BPPARAM
2024-07-23 22:15:01.818365 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:15:01.819958 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:15:01.85796 INFO::Done
2024-07-23 22:15:01.859289 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:01.862318 INFO::ASW Batch was -0.168696224614991 prior to batch effect correction and is now -0.133599782561445 .
2024-07-23 22:15:01.863784 INFO::Total function execution time is 0.0630729198455811 s and adjustment time is 0.043114185333252 s ( 68.36 )
2024-07-23 22:15:01.885356 INFO::Formatting Data.
2024-07-23 22:15:01.886319 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:01.88737 INFO::Removing potential empty rows and columns
2024-07-23 22:15:01.888462 INFO::Found 0 missing values.
2024-07-23 22:15:01.889662 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.
2024-07-23 22:15:01.893376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:01.894121 INFO::Done
2024-07-23 22:15:01.894851 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:01.897768 INFO::Starting hierarchical adjustment
2024-07-23 22:15:01.898618 INFO::Found 2 batches.
2024-07-23 22:15:01.899313 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:15:01.900124 INFO::Using default BPPARAM
2024-07-23 22:15:01.900856 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:15:01.902001 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:15:01.916463 INFO::Done
2024-07-23 22:15:01.917557 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:01.920478 INFO::ASW Batch was 0.328524578665962 prior to batch effect correction and is now -0.0140893920588706 .
2024-07-23 22:15:01.921269 INFO::ASW Label was 0.62422110632664 prior to batch effect correction and is now 0.907433433798709 .
2024-07-23 22:15:01.922196 INFO::Total function execution time is 0.0369789600372314 s and adjustment time is 0.0179040431976318 s ( 48.42 )
2024-07-23 22:15:01.923099 INFO::Formatting Data.
2024-07-23 22:15:01.923892 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:01.924929 INFO::Removing potential empty rows and columns
2024-07-23 22:15:01.926017 INFO::Found 0 missing values.
2024-07-23 22:15:01.927047 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.
2024-07-23 22:15:01.931163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:01.931911 INFO::Done
2024-07-23 22:15:01.932718 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:01.935725 INFO::Starting hierarchical adjustment
2024-07-23 22:15:01.936594 INFO::Found 2 batches.
2024-07-23 22:15:01.937289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:15:01.9381 INFO::Using default BPPARAM
2024-07-23 22:15:01.938796 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:15:01.93985 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:15:01.956122 INFO::Done
2024-07-23 22:15:01.957412 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:01.961838 INFO::ASW Batch was 0.328524578665962 prior to batch effect correction and is now -0.0140893920588706 .
2024-07-23 22:15:01.96316 INFO::ASW Label was 0.62422110632664 prior to batch effect correction and is now 0.907433433798709 .
2024-07-23 22:15:01.964741 INFO::Total function execution time is 0.0415658950805664 s and adjustment time is 0.0195960998535156 s ( 47.14 )
2024-07-23 22:15:02.272639 INFO::Formatting Data.
2024-07-23 22:15:02.274215 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:02.276002 INFO::Removing potential empty rows and columns
2024-07-23 22:15:02.277892 INFO::Found 0 missing values.
2024-07-23 22:15:02.282475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:02.283733 INFO::Done
2024-07-23 22:15:02.284964 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:02.288249 INFO::Starting hierarchical adjustment
2024-07-23 22:15:02.28968 INFO::Found 3 batches.
2024-07-23 22:15:02.290848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:15:02.292155 INFO::Using default BPPARAM
2024-07-23 22:15:02.293325 INFO::Processing subtree level 1
2024-07-23 22:15:05.203528 INFO::Adjusting the last 1 batches sequentially
2024-07-23 22:15:05.20572 INFO::Done
2024-07-23 22:15:05.207051 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:05.210224 INFO::ASW Batch was -0.0688528318923177 prior to batch effect correction and is now -0.0688528318923177 .
2024-07-23 22:15:05.211752 INFO::Total function execution time is 2.93925499916077 s and adjustment time is 2.91621494293213 s ( 99.22 )
2024-07-23 22:15:05.213436 INFO::Formatting Data.
2024-07-23 22:15:05.214694 INFO::Typecasting input to dataframe.
2024-07-23 22:15:05.216111 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:05.217715 INFO::Removing potential empty rows and columns
2024-07-23 22:15:05.219475 INFO::Found 0 missing values.
2024-07-23 22:15:05.223669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:05.224872 INFO::Done
2024-07-23 22:15:05.226071 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:05.229296 INFO::Starting hierarchical adjustment
2024-07-23 22:15:05.230695 INFO::Found 3 batches.
2024-07-23 22:15:05.231848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:15:05.232718 INFO::Using default BPPARAM
2024-07-23 22:15:05.233882 INFO::Processing subtree level 1
2024-07-23 22:15:08.071432 INFO::Adjusting the last 1 batches sequentially
2024-07-23 22:15:08.073691 INFO::Done
2024-07-23 22:15:08.075053 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:08.07834 INFO::ASW Batch was -0.0688528318923177 prior to batch effect correction and is now -0.0688528318923177 .
2024-07-23 22:15:08.079959 INFO::Total function execution time is 2.86649703979492 s and adjustment time is 2.84316396713257 s ( 99.19 )
2024-07-23 22:15:08.098076 INFO::Formatting Data.
2024-07-23 22:15:08.099064 INFO::Typecasting input to dataframe.
2024-07-23 22:15:08.100057 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:08.101097 INFO::Removing potential empty rows and columns
2024-07-23 22:15:08.102218 INFO::Found 0 missing values.
2024-07-23 22:15:08.104756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:08.105612 INFO::Done
2024-07-23 22:15:08.106813 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:08.110034 INFO::Starting hierarchical adjustment
2024-07-23 22:15:08.111431 INFO::Found 3 batches.
2024-07-23 22:15:08.112647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:15:08.113936 INFO::Using default BPPARAM
2024-07-23 22:15:08.115075 INFO::Processing subtree level 1
2024-07-23 22:15:11.069856 INFO::Adjusting the last 1 batches sequentially
2024-07-23 22:15:11.072156 INFO::Done
2024-07-23 22:15:11.073426 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:11.076505 INFO::ASW Batch was -0.122698774349884 prior to batch effect correction and is now -0.122698774349884 .
2024-07-23 22:15:11.077976 INFO::Total function execution time is 2.97993993759155 s and adjustment time is 2.96091389656067 s ( 99.36 )
2024-07-23 22:15:13.82967 INFO::Formatting Data.
2024-07-23 22:15:13.830676 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:13.831974 INFO::Removing potential empty rows and columns
2024-07-23 22:15:13.834239 INFO::Found 1000 missing values.
2024-07-23 22:15:13.847558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:13.848459 INFO::Done
2024-07-23 22:15:13.849189 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:13.855202 INFO::Starting hierarchical adjustment
2024-07-23 22:15:13.856134 INFO::Found 10 batches.
2024-07-23 22:15:13.856846 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:15:13.857622 INFO::Using default BPPARAM
2024-07-23 22:15:13.858327 INFO::Processing subtree level 1
2024-07-23 22:15:16.918976 INFO::Processing subtree level 2
2024-07-23 22:15:19.72222 INFO::Adjusting the last 1 batches sequentially
2024-07-23 22:15:19.72464 INFO::Done
2024-07-23 22:15:19.72599 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:19.735023 INFO::ASW Batch was 0.461190716924125 prior to batch effect correction and is now 0.461190716924125 .
2024-07-23 22:15:19.736394 INFO::ASW Label was 0.355912906237134 prior to batch effect correction and is now 0.355912906237134 .
2024-07-23 22:15:19.738102 INFO::Total function execution time is 5.90845108032227 s and adjustment time is 5.86859107017517 s ( 99.33 )
2024-07-23 22:15:19.739649 INFO::Formatting Data.
2024-07-23 22:15:19.741031 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:19.743072 INFO::Removing potential empty rows and columns
2024-07-23 22:15:19.746795 INFO::Found 1000 missing values.
2024-07-23 22:15:19.769753 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:19.771216 INFO::Done
2024-07-23 22:15:19.77251 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:19.782229 INFO::Starting hierarchical adjustment
2024-07-23 22:15:19.783856 INFO::Found 10 batches.
2024-07-23 22:15:20.542242 INFO::Set up parallel execution backend with 2 workers
2024-07-23 22:15:20.543634 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-23 22:15:23.41667 INFO::Adjusting the last 2 batches sequentially
2024-07-23 22:15:23.418977 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 22:15:23.443565 INFO::Done
2024-07-23 22:15:23.445011 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:23.454421 INFO::ASW Batch was 0.461190716924125 prior to batch effect correction and is now 0.461190716924125 .
2024-07-23 22:15:23.455817 INFO::ASW Label was 0.355912906237134 prior to batch effect correction and is now 0.355912906237134 .
2024-07-23 22:15:23.457453 INFO::Total function execution time is 3.71782279014587 s and adjustment time is 3.65991115570068 s ( 98.44 )
2024-07-23 22:15:26.707251 INFO::Formatting Data.
2024-07-23 22:15:26.708234 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:26.7093 INFO::Removing potential empty rows and columns
2024-07-23 22:15:26.710413 INFO::Found 0 missing values.
2024-07-23 22:15:26.713509 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:26.714245 INFO::Done
2024-07-23 22:15:26.714937 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 22:15:26.717625 INFO::Starting hierarchical adjustment
2024-07-23 22:15:26.71849 INFO::Found 3 batches.
2024-07-23 22:15:26.719211 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 22:15:26.719988 INFO::Using default BPPARAM
2024-07-23 22:15:26.720674 INFO::Processing subtree level 1
2024-07-23 22:15:30.087513 INFO::Adjusting the last 1 batches sequentially
2024-07-23 22:15:30.089639 INFO::Done
2024-07-23 22:15:30.090931 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 22:15:30.094957 INFO::ASW Batch was 0.1015883602336 prior to batch effect correction and is now -0.123666117114898 .
2024-07-23 22:15:30.096219 INFO::ASW Label was -0.192837763837135 prior to batch effect correction and is now 0.01920788600857 .
2024-07-23 22:15:30.097727 INFO::Total function execution time is 3.39049792289734 s and adjustment time is 3.37120890617371 s ( 99.43 )
2024-07-23 22:15:30.310542 INFO::Formatting Data.
2024-07-23 22:15:30.312134 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:30.313962 INFO::Removing potential empty rows and columns
2024-07-23 22:15:30.31583 INFO::Found 2 missing values.
2024-07-23 22:15:30.320272 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:30.321527 INFO::Done
2024-07-23 22:15:30.379789 INFO::Found NA in Reference column
2024-07-23 22:15:30.400367 INFO::Require at least two references per batch.
2024-07-23 22:15:30.433634 INFO::Formatting Data.
2024-07-23 22:15:30.435197 INFO::Recognized SummarizedExperiment
2024-07-23 22:15:30.436535 INFO::Typecasting input to dataframe.
2024-07-23 22:15:30.449385 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:30.451491 INFO::Removing potential empty rows and columns
2024-07-23 22:15:30.456359 INFO::Found 0 missing values.
2024-07-23 22:15:30.465191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:30.466662 INFO::Done
2024-07-23 22:15:30.489405 INFO::Formatting Data.
2024-07-23 22:15:30.490937 INFO::Recognized SummarizedExperiment
2024-07-23 22:15:30.492193 INFO::Typecasting input to dataframe.
2024-07-23 22:15:30.515488 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:30.517749 INFO::Removing potential empty rows and columns
2024-07-23 22:15:30.522684 INFO::Found 0 missing values.
2024-07-23 22:15:30.536608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:30.538095 INFO::Done
2024-07-23 22:15:31.026475 INFO::Formatting Data.
2024-07-23 22:15:31.027992 INFO::Recognized SummarizedExperiment
2024-07-23 22:15:31.029256 INFO::Typecasting input to dataframe.
2024-07-23 22:15:31.052936 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:31.054898 INFO::Removing potential empty rows and columns
2024-07-23 22:15:31.056901 INFO::Found 0 missing values.
2024-07-23 22:15:31.058676 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.
2024-07-23 22:15:31.065205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:31.06661 INFO::Done
2024-07-23 22:15:31.087813 INFO::Formatting Data.
2024-07-23 22:15:31.089387 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:31.091182 INFO::Removing potential empty rows and columns
2024-07-23 22:15:31.093089 INFO::Found 0 missing values.
2024-07-23 22:15:31.097631 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:31.098887 INFO::Done
2024-07-23 22:15:31.121601 INFO::Formatting Data.
2024-07-23 22:15:31.123162 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:31.124901 INFO::Removing potential empty rows and columns
2024-07-23 22:15:31.126465 INFO::Found 0 missing values.
2024-07-23 22:15:31.130762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:31.13197 INFO::Done
2024-07-23 22:15:31.192744 INFO::Formatting Data.
2024-07-23 22:15:31.194458 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:31.196571 INFO::Removing potential empty rows and columns
2024-07-23 22:15:31.198827 INFO::Found 1 missing values.
2024-07-23 22:15:31.201755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:31.202633 INFO::Done
2024-07-23 22:15:31.242406 INFO::Formatting Data.
2024-07-23 22:15:31.244021 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:31.245908 INFO::Removing potential empty rows and columns
2024-07-23 22:15:31.247791 INFO::Found 2 missing values.
2024-07-23 22:15:31.24963 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.
2024-07-23 22:15:31.253253 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:31.254536 INFO::Done
2024-07-23 22:15:31.276656 INFO::Formatting Data.
2024-07-23 22:15:31.278285 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:31.280132 INFO::Removing potential empty rows and columns
2024-07-23 22:15:31.281969 INFO::Found 2 missing values.
2024-07-23 22:15:31.284675 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:31.285883 INFO::Done
2024-07-23 22:15:31.308074 INFO::Formatting Data.
2024-07-23 22:15:31.309645 INFO::Typecasting input to dataframe.
2024-07-23 22:15:31.311321 INFO::Replacing NaNs with NAs.
2024-07-23 22:15:31.313038 INFO::Removing potential empty rows and columns
2024-07-23 22:15:31.314884 INFO::Found 0 missing values.
2024-07-23 22:15:31.319322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 22:15:31.32059 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
30.42 1.59 76.75
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.55 | 0.50 | 18.50 | |
| compute_asw | 0.04 | 0.00 | 0.05 | |
| count_existing | 0.01 | 0.00 | 0.02 | |
| generate_data_covariables | 0.02 | 0.00 | 0.02 | |
| generate_dataset | 0.02 | 0.00 | 0.01 | |