Yannis Schumann
| Snapshot Date: 2024-06-30 14:00 -0400 (Sun, 30 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-03 10:22 -0400 (Wed, 03 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4480 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4511 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4469 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-07-01 12:23:53 -0400 (Mon, 01 Jul 2024) |
| EndedAt: 2024-07-01 12:25:13 -0400 (Mon, 01 Jul 2024) |
| EllapsedTime: 80.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 29.067 1.076 20.588
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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")
2024-07-01 12:24:52.529378 INFO::Formatting Data.
2024-07-01 12:24:52.53372 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:52.546091 INFO::Removing potential empty rows and columns
2024-07-01 12:24:52.936165 INFO::Found 0 missing values.
2024-07-01 12:24:52.941216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:52.942007 INFO::Done
2024-07-01 12:24:52.942587 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:52.961493 INFO::Starting hierarchical adjustment
2024-07-01 12:24:52.962502 INFO::Found 3 batches.
2024-07-01 12:24:52.963023 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:52.964462 INFO::Using default BPPARAM
2024-07-01 12:24:52.964979 INFO::Processing subtree level 1
2024-07-01 12:24:53.115381 INFO::Adjusting the last 1 batches sequentially
2024-07-01 12:24:53.119953 INFO::Done
2024-07-01 12:24:53.120957 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:53.126023 INFO::ASW Batch was -0.0696667569724287 prior to batch effect correction and is now -0.0696667569724287 .
2024-07-01 12:24:53.1279 INFO::Total function execution time is 0.599380970001221 s and adjustment time is 0.157592058181763 s ( 26.29 )
2024-07-01 12:24:53.151771 INFO::Formatting Data.
2024-07-01 12:24:53.152822 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:53.154071 INFO::Removing potential empty rows and columns
2024-07-01 12:24:53.155752 INFO::Found 0 missing values.
2024-07-01 12:24:53.157015 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.
2024-07-01 12:24:53.171716 INFO::Formatting Data.
2024-07-01 12:24:53.172816 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:53.173926 INFO::Removing potential empty rows and columns
2024-07-01 12:24:53.175818 INFO::Found 0 missing values.
2024-07-01 12:24:53.177044 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.
2024-07-01 12:24:53.198356 INFO::Formatting Data.
2024-07-01 12:24:53.199245 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:53.200197 INFO::Removing potential empty rows and columns
2024-07-01 12:24:53.201274 INFO::Found 0 missing values.
2024-07-01 12:24:53.202201 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.
2024-07-01 12:24:53.206411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:53.207107 INFO::Done
2024-07-01 12:24:53.207639 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:53.209892 INFO::Starting hierarchical adjustment
2024-07-01 12:24:53.21066 INFO::Found 2 batches.
2024-07-01 12:24:53.211174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:53.211922 INFO::Using default BPPARAM
2024-07-01 12:24:53.212533 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:53.213435 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:53.242486 INFO::Done
2024-07-01 12:24:53.243381 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:53.245688 INFO::ASW Batch was 0.0437310563334581 prior to batch effect correction and is now -0.0838310820087272 .
2024-07-01 12:24:53.246602 INFO::Total function execution time is 0.0484189987182617 s and adjustment time is 0.0318729877471924 s ( 65.83 )
2024-07-01 12:24:53.249971 INFO::Formatting Data.
2024-07-01 12:24:53.250685 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:53.260577 INFO::Formatting Data.
2024-07-01 12:24:53.261444 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:53.26234 INFO::Removing potential empty rows and columns
2024-07-01 12:24:53.263372 INFO::Found 0 missing values.
2024-07-01 12:24:53.266089 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:53.266736 INFO::Done
2024-07-01 12:24:53.2672 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:53.269587 INFO::Starting hierarchical adjustment
2024-07-01 12:24:53.270363 INFO::Found 2 batches.
2024-07-01 12:24:53.270841 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:53.271444 INFO::Using default BPPARAM
2024-07-01 12:24:53.271906 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:53.272742 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:53.288628 INFO::Done
2024-07-01 12:24:53.28946 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:53.291724 INFO::ASW Batch was 0.0221755879896523 prior to batch effect correction and is now -0.11966249408908 .
2024-07-01 12:24:53.292653 INFO::Total function execution time is 0.0322029590606689 s and adjustment time is 0.0183510780334473 s ( 56.99 )
2024-07-01 12:24:53.293709 INFO::Formatting Data.
2024-07-01 12:24:53.29422 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:53.295058 INFO::Removing potential empty rows and columns
2024-07-01 12:24:53.29606 INFO::Found 0 missing values.
2024-07-01 12:24:53.298797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:53.299376 INFO::Done
2024-07-01 12:24:53.299849 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:53.30214 INFO::Starting hierarchical adjustment
2024-07-01 12:24:53.302827 INFO::Found 2 batches.
2024-07-01 12:24:53.303308 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:53.303872 INFO::Using default BPPARAM
2024-07-01 12:24:53.304314 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:53.305143 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:53.321391 INFO::Done
2024-07-01 12:24:53.32221 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:53.324357 INFO::ASW Batch was 0.0221755879896523 prior to batch effect correction and is now -0.11966249408908 .
2024-07-01 12:24:53.325214 INFO::Total function execution time is 0.0314738750457764 s and adjustment time is 0.0186400413513184 s ( 59.22 )
2024-07-01 12:24:56.01103 INFO::Formatting Data.
2024-07-01 12:24:56.011822 INFO::Recognized SummarizedExperiment
2024-07-01 12:24:56.012246 INFO::Typecasting input to dataframe.
2024-07-01 12:24:56.916786 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:56.918048 INFO::Removing potential empty rows and columns
2024-07-01 12:24:56.921081 INFO::Found 0 missing values.
2024-07-01 12:24:56.926745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:56.927307 INFO::Done
2024-07-01 12:24:56.927715 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:56.931042 INFO::Starting hierarchical adjustment
2024-07-01 12:24:56.931691 INFO::Found 2 batches.
2024-07-01 12:24:56.932099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:56.933169 INFO::Using default BPPARAM
2024-07-01 12:24:56.933583 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:56.934382 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:56.981305 INFO::Done
2024-07-01 12:24:56.981952 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:56.985372 INFO::ASW Batch was -0.0111507632713689 prior to batch effect correction and is now -0.0900426819545343 .
2024-07-01 12:24:56.986107 INFO::Total function execution time is 0.975423812866211 s and adjustment time is 0.0497140884399414 s ( 5.1 )
2024-07-01 12:24:57.00214 INFO::Formatting Data.
2024-07-01 12:24:57.002906 INFO::Recognized SummarizedExperiment
2024-07-01 12:24:57.003347 INFO::Typecasting input to dataframe.
2024-07-01 12:24:57.011531 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:57.012607 INFO::Removing potential empty rows and columns
2024-07-01 12:24:57.015713 INFO::Found 0 missing values.
2024-07-01 12:24:57.021535 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:57.022102 INFO::Done
2024-07-01 12:24:57.022535 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:57.025949 INFO::Starting hierarchical adjustment
2024-07-01 12:24:57.026558 INFO::Found 2 batches.
2024-07-01 12:24:57.026968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:57.027455 INFO::Using default BPPARAM
2024-07-01 12:24:57.027848 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:57.028631 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:57.050626 INFO::Done
2024-07-01 12:24:57.051296 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:57.054631 INFO::ASW Batch was -0.0108742287536211 prior to batch effect correction and is now -0.0108742287536211 .
2024-07-01 12:24:57.055398 INFO::Total function execution time is 0.0532889366149902 s and adjustment time is 0.024122953414917 s ( 45.27 )
2024-07-01 12:24:57.072146 INFO::Formatting Data.
2024-07-01 12:24:57.072817 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:57.073537 INFO::Removing potential empty rows and columns
2024-07-01 12:24:57.074356 INFO::Found 0 missing values.
2024-07-01 12:24:57.076611 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:57.077042 INFO::Done
2024-07-01 12:24:57.07744 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:57.079174 INFO::Starting hierarchical adjustment
2024-07-01 12:24:57.079741 INFO::Found 3 batches.
2024-07-01 12:24:57.080133 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:57.080607 INFO::Using default BPPARAM
2024-07-01 12:24:57.080977 INFO::Processing subtree level 1
2024-07-01 12:24:57.259629 INFO::Adjusting the last 1 batches sequentially
2024-07-01 12:24:57.263623 INFO::Done
2024-07-01 12:24:57.265148 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:57.270436 INFO::ASW Batch was -0.0530880087990159 prior to batch effect correction and is now -0.15888014528009 .
2024-07-01 12:24:57.27243 INFO::Total function execution time is 0.200093030929565 s and adjustment time is 0.183889150619507 s ( 91.9 )
2024-07-01 12:24:57.298412 INFO::Skipping initial DF formatting
2024-07-01 12:24:57.299469 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:57.305315 INFO::Starting hierarchical adjustment
2024-07-01 12:24:57.306629 INFO::Found 5 batches.
2024-07-01 12:24:57.307414 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:57.308132 INFO::Using default BPPARAM
2024-07-01 12:24:57.308736 INFO::Processing subtree level 1
2024-07-01 12:24:57.442737 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:57.446878 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:57.477638 INFO::Done
2024-07-01 12:24:57.478511 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:57.484826 INFO::ASW Batch was 0.487952956808065 prior to batch effect correction and is now 0.487952956808065 .
2024-07-01 12:24:57.485705 INFO::ASW Label was 0.407195556265739 prior to batch effect correction and is now 0.407195556265739 .
2024-07-01 12:24:57.486911 INFO::Total function execution time is 0.18858003616333 s and adjustment time is 0.17126202583313 s ( 90.82 )
2024-07-01 12:24:57.511305 INFO::Formatting Data.
2024-07-01 12:24:57.512181 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:57.513183 INFO::Removing potential empty rows and columns
2024-07-01 12:24:57.514294 INFO::Found 0 missing values.
2024-07-01 12:24:57.518013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:57.518652 INFO::Done
2024-07-01 12:24:57.519169 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:57.522065 INFO::Starting hierarchical adjustment
2024-07-01 12:24:57.522759 INFO::Found 5 batches.
2024-07-01 12:24:57.523246 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:57.523928 INFO::Using default BPPARAM
2024-07-01 12:24:57.524417 INFO::Processing subtree level 1
2024-07-01 12:24:57.633018 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:57.635707 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:57.656996 INFO::Done
2024-07-01 12:24:57.657814 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:57.661958 INFO::ASW Batch was 0.577276689335085 prior to batch effect correction and is now -0.0806184314671766 .
2024-07-01 12:24:57.662661 INFO::ASW Label was 0.209667979216599 prior to batch effect correction and is now 0.836955664439726 .
2024-07-01 12:24:57.663648 INFO::Total function execution time is 0.152430057525635 s and adjustment time is 0.134317874908447 s ( 88.12 )
2024-07-01 12:24:57.66452 INFO::Formatting Data.
2024-07-01 12:24:57.665111 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:57.666119 INFO::Removing potential empty rows and columns
2024-07-01 12:24:57.667306 INFO::Found 0 missing values.
2024-07-01 12:24:57.671066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:57.671698 INFO::Done
2024-07-01 12:24:57.672271 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:57.675175 INFO::Starting hierarchical adjustment
2024-07-01 12:24:57.675958 INFO::Found 5 batches.
2024-07-01 12:24:57.676454 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:57.677059 INFO::Using default BPPARAM
2024-07-01 12:24:57.677575 INFO::Processing subtree level 1
2024-07-01 12:24:57.783775 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:57.787059 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:57.808544 INFO::Done
2024-07-01 12:24:57.809459 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:57.813339 INFO::ASW Batch was 0.577276689335085 prior to batch effect correction and is now -0.0806184314671766 .
2024-07-01 12:24:57.814052 INFO::ASW Label was 0.209667979216599 prior to batch effect correction and is now 0.836955664439726 .
2024-07-01 12:24:57.815089 INFO::Total function execution time is 0.150445938110352 s and adjustment time is 0.132688999176025 s ( 88.2 )
2024-07-01 12:24:57.831836 INFO::Formatting Data.
2024-07-01 12:24:57.832677 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:57.833546 INFO::Removing potential empty rows and columns
2024-07-01 12:24:57.834543 INFO::Found 0 missing values.
2024-07-01 12:24:57.838215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:57.838818 INFO::Done
2024-07-01 12:24:57.839329 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:57.842201 INFO::Starting hierarchical adjustment
2024-07-01 12:24:57.842913 INFO::Found 5 batches.
2024-07-01 12:24:57.843378 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:57.84397 INFO::Using default BPPARAM
2024-07-01 12:24:57.844438 INFO::Processing subtree level 1
2024-07-01 12:24:57.960303 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:57.963942 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:57.983141 INFO::Done
2024-07-01 12:24:57.983915 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:57.987326 INFO::ASW Batch was 0.400234769540062 prior to batch effect correction and is now -0.0494985511308053 .
2024-07-01 12:24:57.987951 INFO::ASW Label was 0.249900050026474 prior to batch effect correction and is now 0.802917384443477 .
2024-07-01 12:24:57.988896 INFO::Total function execution time is 0.157142162322998 s and adjustment time is 0.140323877334595 s ( 89.3 )
2024-07-01 12:24:57.989712 INFO::Formatting Data.
2024-07-01 12:24:57.990297 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:57.991182 INFO::Removing potential empty rows and columns
2024-07-01 12:24:57.992165 INFO::Found 0 missing values.
2024-07-01 12:24:57.99572 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:57.996322 INFO::Done
2024-07-01 12:24:57.996786 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:57.999709 INFO::Starting hierarchical adjustment
2024-07-01 12:24:58.000412 INFO::Found 5 batches.
2024-07-01 12:24:58.000887 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:58.001557 INFO::Using default BPPARAM
2024-07-01 12:24:58.002005 INFO::Processing subtree level 1
2024-07-01 12:24:58.126931 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:58.129708 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:58.149619 INFO::Done
2024-07-01 12:24:58.150492 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:58.154205 INFO::ASW Batch was 0.400234769540062 prior to batch effect correction and is now -0.0494985511308053 .
2024-07-01 12:24:58.154942 INFO::ASW Label was 0.249900050026474 prior to batch effect correction and is now 0.802917384443477 .
2024-07-01 12:24:58.155943 INFO::Total function execution time is 0.166152954101562 s and adjustment time is 0.149283885955811 s ( 89.85 )
2024-07-01 12:24:58.173153 INFO::Formatting Data.
2024-07-01 12:24:58.174032 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:58.175008 INFO::Removing potential empty rows and columns
2024-07-01 12:24:58.176076 INFO::Found 0 missing values.
2024-07-01 12:24:58.178654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:58.179194 INFO::Done
2024-07-01 12:24:58.179769 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:58.182616 INFO::Starting hierarchical adjustment
2024-07-01 12:24:58.183422 INFO::Found 2 batches.
2024-07-01 12:24:58.183933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:58.184554 INFO::Using default BPPARAM
2024-07-01 12:24:58.185002 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:58.185829 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:58.200305 INFO::Done
2024-07-01 12:24:58.201023 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:58.2039 INFO::ASW Batch was 0.606338074232197 prior to batch effect correction and is now 0.0144173486227631 .
2024-07-01 12:24:58.204488 INFO::ASW Label was 0.517865329114328 prior to batch effect correction and is now 0.922464481803503 .
2024-07-01 12:24:58.205255 INFO::Total function execution time is 0.0322918891906738 s and adjustment time is 0.0170161724090576 s ( 52.69 )
2024-07-01 12:24:58.20593 INFO::Formatting Data.
2024-07-01 12:24:58.206445 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:58.207262 INFO::Removing potential empty rows and columns
2024-07-01 12:24:58.208119 INFO::Found 0 missing values.
2024-07-01 12:24:58.210487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:58.210997 INFO::Done
2024-07-01 12:24:58.211449 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:58.214105 INFO::Starting hierarchical adjustment
2024-07-01 12:24:58.214798 INFO::Found 2 batches.
2024-07-01 12:24:58.215237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:58.215767 INFO::Using default BPPARAM
2024-07-01 12:24:58.216193 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:58.216963 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:58.231402 INFO::Done
2024-07-01 12:24:58.23215 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:58.234996 INFO::ASW Batch was 0.606338074232197 prior to batch effect correction and is now 0.0144173486227631 .
2024-07-01 12:24:58.235544 INFO::ASW Label was 0.517865329114328 prior to batch effect correction and is now 0.922464481803503 .
2024-07-01 12:24:58.236294 INFO::Total function execution time is 0.0303070545196533 s and adjustment time is 0.0167059898376465 s ( 55.12 )
2024-07-01 12:24:58.248339 INFO::Formatting Data.
2024-07-01 12:24:58.249075 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:58.249973 INFO::Removing potential empty rows and columns
2024-07-01 12:24:58.250833 INFO::Found 0 missing values.
2024-07-01 12:24:58.252696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:58.253164 INFO::Done
2024-07-01 12:24:58.25362 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:58.255467 INFO::Starting hierarchical adjustment
2024-07-01 12:24:58.256141 INFO::Found 2 batches.
2024-07-01 12:24:58.256588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:58.25713 INFO::Using default BPPARAM
2024-07-01 12:24:58.257554 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:58.258316 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:58.291286 INFO::Done
2024-07-01 12:24:58.292083 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:58.294108 INFO::ASW Batch was -0.172982743021112 prior to batch effect correction and is now -0.189800652611426 .
2024-07-01 12:24:58.294929 INFO::Total function execution time is 0.0466952323913574 s and adjustment time is 0.0352180004119873 s ( 75.42 )
2024-07-01 12:24:58.30763 INFO::Formatting Data.
2024-07-01 12:24:58.308374 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:58.309201 INFO::Removing potential empty rows and columns
2024-07-01 12:24:58.310189 INFO::Found 0 missing values.
2024-07-01 12:24:58.311555 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.
2024-07-01 12:24:58.315791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:58.316399 INFO::Done
2024-07-01 12:24:58.316906 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:58.31976 INFO::Starting hierarchical adjustment
2024-07-01 12:24:58.320419 INFO::Found 2 batches.
2024-07-01 12:24:58.320888 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:58.321438 INFO::Using default BPPARAM
2024-07-01 12:24:58.321881 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:58.322742 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:58.339515 INFO::Done
2024-07-01 12:24:58.340288 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:58.343295 INFO::ASW Batch was 0.590820885969152 prior to batch effect correction and is now 0.00426753236799323 .
2024-07-01 12:24:58.34394 INFO::ASW Label was 0.503184729618202 prior to batch effect correction and is now 0.912728782752274 .
2024-07-01 12:24:58.344711 INFO::Total function execution time is 0.0371870994567871 s and adjustment time is 0.0191631317138672 s ( 51.53 )
2024-07-01 12:24:58.345433 INFO::Formatting Data.
2024-07-01 12:24:58.345987 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:58.346877 INFO::Removing potential empty rows and columns
2024-07-01 12:24:58.347863 INFO::Found 0 missing values.
2024-07-01 12:24:58.348721 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.
2024-07-01 12:24:58.352724 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:58.354686 INFO::Done
2024-07-01 12:24:58.355431 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:58.358623 INFO::Starting hierarchical adjustment
2024-07-01 12:24:58.365731 INFO::Found 2 batches.
2024-07-01 12:24:58.371501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:58.377577 INFO::Using default BPPARAM
2024-07-01 12:24:58.380716 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:24:58.387392 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:24:58.404437 INFO::Done
2024-07-01 12:24:58.406011 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:58.410022 INFO::ASW Batch was 0.590820885969152 prior to batch effect correction and is now 0.00426753236799323 .
2024-07-01 12:24:58.411669 INFO::ASW Label was 0.503184729618202 prior to batch effect correction and is now 0.912728782752274 .
2024-07-01 12:24:58.413115 INFO::Total function execution time is 0.0674948692321777 s and adjustment time is 0.0391881465911865 s ( 58.06 )
2024-07-01 12:24:58.64642 INFO::Formatting Data.
2024-07-01 12:24:58.647682 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:58.649161 INFO::Removing potential empty rows and columns
2024-07-01 12:24:58.650506 INFO::Found 0 missing values.
2024-07-01 12:24:58.65393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:58.654451 INFO::Done
2024-07-01 12:24:58.655722 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:58.658727 INFO::Starting hierarchical adjustment
2024-07-01 12:24:58.660524 INFO::Found 3 batches.
2024-07-01 12:24:58.661842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:58.66394 INFO::Using default BPPARAM
2024-07-01 12:24:58.66538 INFO::Processing subtree level 1
2024-07-01 12:24:58.798865 INFO::Adjusting the last 1 batches sequentially
2024-07-01 12:24:58.801297 INFO::Done
2024-07-01 12:24:58.801901 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:58.805898 INFO::ASW Batch was 0.0375060774518399 prior to batch effect correction and is now 0.0375060774518399 .
2024-07-01 12:24:58.808106 INFO::Total function execution time is 0.161745071411133 s and adjustment time is 0.14104700088501 s ( 87.2 )
2024-07-01 12:24:58.809185 INFO::Formatting Data.
2024-07-01 12:24:58.809748 INFO::Typecasting input to dataframe.
2024-07-01 12:24:58.810435 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:58.811325 INFO::Removing potential empty rows and columns
2024-07-01 12:24:58.812693 INFO::Found 0 missing values.
2024-07-01 12:24:58.815924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:58.816539 INFO::Done
2024-07-01 12:24:58.817089 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:58.819152 INFO::Starting hierarchical adjustment
2024-07-01 12:24:58.82003 INFO::Found 3 batches.
2024-07-01 12:24:58.820522 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:58.82113 INFO::Using default BPPARAM
2024-07-01 12:24:58.821578 INFO::Processing subtree level 1
2024-07-01 12:24:58.926797 INFO::Adjusting the last 1 batches sequentially
2024-07-01 12:24:58.929341 INFO::Done
2024-07-01 12:24:58.92992 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:58.933807 INFO::ASW Batch was 0.0375060774518399 prior to batch effect correction and is now 0.0375060774518399 .
2024-07-01 12:24:58.935597 INFO::Total function execution time is 0.126336812973022 s and adjustment time is 0.109627962112427 s ( 86.77 )
2024-07-01 12:24:58.956363 INFO::Formatting Data.
2024-07-01 12:24:58.957253 INFO::Typecasting input to dataframe.
2024-07-01 12:24:58.958091 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:58.959092 INFO::Removing potential empty rows and columns
2024-07-01 12:24:58.960693 INFO::Found 0 missing values.
2024-07-01 12:24:58.96347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:58.964047 INFO::Done
2024-07-01 12:24:58.964538 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:58.966568 INFO::Starting hierarchical adjustment
2024-07-01 12:24:58.967302 INFO::Found 3 batches.
2024-07-01 12:24:58.96779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:58.968463 INFO::Using default BPPARAM
2024-07-01 12:24:58.968919 INFO::Processing subtree level 1
2024-07-01 12:24:59.071263 INFO::Adjusting the last 1 batches sequentially
2024-07-01 12:24:59.074649 INFO::Done
2024-07-01 12:24:59.075273 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:59.080221 INFO::ASW Batch was -0.0863418667598867 prior to batch effect correction and is now -0.0863418667598867 .
2024-07-01 12:24:59.082112 INFO::Total function execution time is 0.125885009765625 s and adjustment time is 0.10745096206665 s ( 85.36 )
2024-07-01 12:24:59.211009 INFO::Formatting Data.
2024-07-01 12:24:59.211706 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:59.212456 INFO::Removing potential empty rows and columns
2024-07-01 12:24:59.214533 INFO::Found 1000 missing values.
2024-07-01 12:24:59.224272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:59.22495 INFO::Done
2024-07-01 12:24:59.225192 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:59.228358 INFO::Starting hierarchical adjustment
2024-07-01 12:24:59.228932 INFO::Found 10 batches.
2024-07-01 12:24:59.229174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:24:59.229524 INFO::Using default BPPARAM
2024-07-01 12:24:59.229739 INFO::Processing subtree level 1
2024-07-01 12:24:59.334046 INFO::Processing subtree level 2
2024-07-01 12:24:59.483733 INFO::Adjusting the last 1 batches sequentially
2024-07-01 12:24:59.486415 INFO::Done
2024-07-01 12:24:59.486685 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:24:59.491164 INFO::ASW Batch was 0.530932122382096 prior to batch effect correction and is now 0.530932122382096 .
2024-07-01 12:24:59.491845 INFO::ASW Label was 0.327774476312364 prior to batch effect correction and is now 0.327774476312364 .
2024-07-01 12:24:59.493705 INFO::Total function execution time is 0.282764196395874 s and adjustment time is 0.257560968399048 s ( 91.09 )
2024-07-01 12:24:59.494201 INFO::Formatting Data.
2024-07-01 12:24:59.494428 INFO::Replacing NaNs with NAs.
2024-07-01 12:24:59.495017 INFO::Removing potential empty rows and columns
2024-07-01 12:24:59.496321 INFO::Found 1000 missing values.
2024-07-01 12:24:59.50452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:24:59.505358 INFO::Done
2024-07-01 12:24:59.505666 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:24:59.508553 INFO::Starting hierarchical adjustment
2024-07-01 12:24:59.509036 INFO::Found 10 batches.
2024-07-01 12:25:00.770127 INFO::Set up parallel execution backend with 2 workers
2024-07-01 12:25:00.7713 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-01 12:25:02.221192 INFO::Adjusting the last 2 batches sequentially
2024-07-01 12:25:02.222852 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-01 12:25:02.239995 INFO::Done
2024-07-01 12:25:02.240773 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:25:02.246384 INFO::ASW Batch was 0.530932122382096 prior to batch effect correction and is now 0.530932122382096 .
2024-07-01 12:25:02.247057 INFO::ASW Label was 0.327774476312364 prior to batch effect correction and is now 0.327774476312364 .
2024-07-01 12:25:02.247784 INFO::Total function execution time is 2.75349497795105 s and adjustment time is 2.73092794418335 s ( 99.18 )
2024-07-01 12:25:02.427047 INFO::Formatting Data.
2024-07-01 12:25:02.428073 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:02.429183 INFO::Removing potential empty rows and columns
2024-07-01 12:25:02.430408 INFO::Found 0 missing values.
2024-07-01 12:25:02.434029 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:02.434606 INFO::Done
2024-07-01 12:25:02.435079 INFO::Acquiring quality metrics before batch effect correction.
2024-07-01 12:25:02.437987 INFO::Starting hierarchical adjustment
2024-07-01 12:25:02.438784 INFO::Found 3 batches.
2024-07-01 12:25:02.439344 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-01 12:25:02.440193 INFO::Using default BPPARAM
2024-07-01 12:25:02.442345 INFO::Processing subtree level 1
2024-07-01 12:25:02.582894 INFO::Adjusting the last 1 batches sequentially
2024-07-01 12:25:02.587879 INFO::Done
2024-07-01 12:25:02.58865 INFO::Acquiring quality metrics after batch effect correction.
2024-07-01 12:25:02.595754 INFO::ASW Batch was 0.252261731661671 prior to batch effect correction and is now -0.132167342580626 .
2024-07-01 12:25:02.597049 INFO::ASW Label was -0.229375466466704 prior to batch effect correction and is now 0.00652716240146421 .
2024-07-01 12:25:02.599435 INFO::Total function execution time is 0.172326803207397 s and adjustment time is 0.149231910705566 s ( 86.6 )
2024-07-01 12:25:02.757554 INFO::Formatting Data.
2024-07-01 12:25:02.758832 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:02.760345 INFO::Removing potential empty rows and columns
2024-07-01 12:25:02.761907 INFO::Found 2 missing values.
2024-07-01 12:25:02.765069 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:02.765723 INFO::Done
2024-07-01 12:25:02.804129 INFO::Found NA in Reference column
2024-07-01 12:25:02.819586 INFO::Require at least two references per batch.
2024-07-01 12:25:02.848088 INFO::Formatting Data.
2024-07-01 12:25:02.849027 INFO::Recognized SummarizedExperiment
2024-07-01 12:25:02.849536 INFO::Typecasting input to dataframe.
2024-07-01 12:25:02.862267 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:02.863874 INFO::Removing potential empty rows and columns
2024-07-01 12:25:02.869217 INFO::Found 0 missing values.
2024-07-01 12:25:02.878906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:02.88001 INFO::Done
2024-07-01 12:25:02.896036 INFO::Formatting Data.
2024-07-01 12:25:02.896894 INFO::Recognized SummarizedExperiment
2024-07-01 12:25:02.897395 INFO::Typecasting input to dataframe.
2024-07-01 12:25:02.915741 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:02.917133 INFO::Removing potential empty rows and columns
2024-07-01 12:25:02.921171 INFO::Found 0 missing values.
2024-07-01 12:25:02.934435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:02.935344 INFO::Done
2024-07-01 12:25:02.953422 INFO::Formatting Data.
2024-07-01 12:25:02.954343 INFO::Recognized SummarizedExperiment
2024-07-01 12:25:02.954876 INFO::Typecasting input to dataframe.
2024-07-01 12:25:02.973352 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:02.97452 INFO::Removing potential empty rows and columns
2024-07-01 12:25:02.975659 INFO::Found 0 missing values.
2024-07-01 12:25:02.976651 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.
2024-07-01 12:25:02.981689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:02.98245 INFO::Done
2024-07-01 12:25:02.995807 INFO::Formatting Data.
2024-07-01 12:25:02.996849 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:02.997839 INFO::Removing potential empty rows and columns
2024-07-01 12:25:02.998941 INFO::Found 0 missing values.
2024-07-01 12:25:03.001936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:03.002617 INFO::Done
2024-07-01 12:25:03.016876 INFO::Formatting Data.
2024-07-01 12:25:03.017754 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:03.01854 INFO::Removing potential empty rows and columns
2024-07-01 12:25:03.019551 INFO::Found 0 missing values.
2024-07-01 12:25:03.022241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:03.022777 INFO::Done
2024-07-01 12:25:03.057484 INFO::Formatting Data.
2024-07-01 12:25:03.058569 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:03.059769 INFO::Removing potential empty rows and columns
2024-07-01 12:25:03.06109 INFO::Found 1 missing values.
2024-07-01 12:25:03.064959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:03.065572 INFO::Done
2024-07-01 12:25:03.089693 INFO::Formatting Data.
2024-07-01 12:25:03.090728 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:03.091846 INFO::Removing potential empty rows and columns
2024-07-01 12:25:03.093042 INFO::Found 2 missing values.
2024-07-01 12:25:03.094127 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.
2024-07-01 12:25:03.096908 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:03.097636 INFO::Done
2024-07-01 12:25:03.110072 INFO::Formatting Data.
2024-07-01 12:25:03.110901 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:03.111727 INFO::Removing potential empty rows and columns
2024-07-01 12:25:03.112604 INFO::Found 2 missing values.
2024-07-01 12:25:03.114102 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:03.1146 INFO::Done
2024-07-01 12:25:03.126745 INFO::Formatting Data.
2024-07-01 12:25:03.127591 INFO::Typecasting input to dataframe.
2024-07-01 12:25:03.128358 INFO::Replacing NaNs with NAs.
2024-07-01 12:25:03.129349 INFO::Removing potential empty rows and columns
2024-07-01 12:25:03.130387 INFO::Found 0 missing values.
2024-07-01 12:25:03.133588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-01 12:25:03.134208 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.188 3.802 24.504
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.067 | 1.076 | 20.588 | |
| compute_asw | 0.031 | 0.002 | 0.032 | |
| count_existing | 0.016 | 0.001 | 0.017 | |
| generate_data_covariables | 0.014 | 0.001 | 0.015 | |
| generate_dataset | 0.014 | 0.001 | 0.014 | |