Yannis Schumann
| Snapshot Date: 2024-10-09 14:00 -0400 (Wed, 09 Oct 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 2024-10-11 20:42 -0400 (Fri, 11 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
| 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 12.7.5 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: 2024-10-10 13:04:12 -0400 (Thu, 10 Oct 2024) |
| EndedAt: 2024-10-10 13:05:45 -0400 (Thu, 10 Oct 2024) |
| EllapsedTime: 92.8 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 4.4.1 (2024-06-14)
* 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 30.33 1.549 23.341
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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")
2024-10-10 13:05:21.299925 INFO::Formatting Data.
2024-10-10 13:05:21.305032 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:21.32106 INFO::Removing potential empty rows and columns
2024-10-10 13:05:21.733536 INFO::Found 0 missing values.
2024-10-10 13:05:21.737281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:21.73797 INFO::Done
2024-10-10 13:05:21.738702 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:21.761467 INFO::Starting hierarchical adjustment
2024-10-10 13:05:21.7626 INFO::Found 3 batches.
2024-10-10 13:05:21.763187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:21.764986 INFO::Using default BPPARAM
2024-10-10 13:05:21.765756 INFO::Processing subtree level 1
2024-10-10 13:05:21.965262 INFO::Adjusting the last 1 batches sequentially
2024-10-10 13:05:21.971414 INFO::Done
2024-10-10 13:05:21.972768 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:21.979313 INFO::ASW Batch was -0.0798878375639333 prior to batch effect correction and is now -0.0798878375639333 .
2024-10-10 13:05:21.981924 INFO::Total function execution time is 0.682936906814575 s and adjustment time is 0.208968162536621 s ( 30.6 )
2024-10-10 13:05:22.007841 INFO::Formatting Data.
2024-10-10 13:05:22.008828 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:22.009909 INFO::Removing potential empty rows and columns
2024-10-10 13:05:22.011736 INFO::Found 0 missing values.
2024-10-10 13:05:22.014111 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-10 13:05:22.031383 INFO::Formatting Data.
2024-10-10 13:05:22.032423 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:22.033466 INFO::Removing potential empty rows and columns
2024-10-10 13:05:22.03478 INFO::Found 0 missing values.
2024-10-10 13:05:22.035961 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-10 13:05:22.064736 INFO::Formatting Data.
2024-10-10 13:05:22.065758 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:22.066836 INFO::Removing potential empty rows and columns
2024-10-10 13:05:22.06867 INFO::Found 0 missing values.
2024-10-10 13:05:22.070412 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-10 13:05:22.077657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:22.078612 INFO::Done
2024-10-10 13:05:22.079289 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:22.082266 INFO::Starting hierarchical adjustment
2024-10-10 13:05:22.083145 INFO::Found 2 batches.
2024-10-10 13:05:22.083765 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:22.084735 INFO::Using default BPPARAM
2024-10-10 13:05:22.085308 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:22.086319 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:22.126784 INFO::Done
2024-10-10 13:05:22.127725 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:22.134552 INFO::ASW Batch was -0.02509092653169 prior to batch effect correction and is now -0.124033252772153 .
2024-10-10 13:05:22.136001 INFO::Total function execution time is 0.0714747905731201 s and adjustment time is 0.0437259674072266 s ( 61.18 )
2024-10-10 13:05:22.140177 INFO::Formatting Data.
2024-10-10 13:05:22.141014 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:22.15212 INFO::Formatting Data.
2024-10-10 13:05:22.153251 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:22.154593 INFO::Removing potential empty rows and columns
2024-10-10 13:05:22.155854 INFO::Found 0 missing values.
2024-10-10 13:05:22.15918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:22.159757 INFO::Done
2024-10-10 13:05:22.160641 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:22.164613 INFO::Starting hierarchical adjustment
2024-10-10 13:05:22.165401 INFO::Found 2 batches.
2024-10-10 13:05:22.165933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:22.166932 INFO::Using default BPPARAM
2024-10-10 13:05:22.167627 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:22.168862 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:22.184983 INFO::Done
2024-10-10 13:05:22.185777 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:22.187923 INFO::ASW Batch was -0.0690541419022784 prior to batch effect correction and is now -0.122211021967311 .
2024-10-10 13:05:22.188766 INFO::Total function execution time is 0.0367698669433594 s and adjustment time is 0.0196988582611084 s ( 53.57 )
2024-10-10 13:05:22.189744 INFO::Formatting Data.
2024-10-10 13:05:22.190312 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:22.191113 INFO::Removing potential empty rows and columns
2024-10-10 13:05:22.192247 INFO::Found 0 missing values.
2024-10-10 13:05:22.19547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:22.196374 INFO::Done
2024-10-10 13:05:22.199694 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:22.20224 INFO::Starting hierarchical adjustment
2024-10-10 13:05:22.202951 INFO::Found 2 batches.
2024-10-10 13:05:22.203447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:22.204038 INFO::Using default BPPARAM
2024-10-10 13:05:22.204475 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:22.205269 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:22.224326 INFO::Done
2024-10-10 13:05:22.225156 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:22.228093 INFO::ASW Batch was -0.0690541419022784 prior to batch effect correction and is now -0.122211021967311 .
2024-10-10 13:05:22.229208 INFO::Total function execution time is 0.0394268035888672 s and adjustment time is 0.0214560031890869 s ( 54.42 )
2024-10-10 13:05:25.12437 INFO::Formatting Data.
2024-10-10 13:05:25.125231 INFO::Recognized SummarizedExperiment
2024-10-10 13:05:25.12569 INFO::Typecasting input to dataframe.
2024-10-10 13:05:25.16617 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:25.167533 INFO::Removing potential empty rows and columns
2024-10-10 13:05:25.210671 INFO::Found 0 missing values.
2024-10-10 13:05:25.217068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:25.217648 INFO::Done
2024-10-10 13:05:25.218073 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:25.223405 INFO::Starting hierarchical adjustment
2024-10-10 13:05:25.224329 INFO::Found 2 batches.
2024-10-10 13:05:25.224812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:25.22604 INFO::Using default BPPARAM
2024-10-10 13:05:25.226485 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:25.227404 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:25.288003 INFO::Done
2024-10-10 13:05:25.288836 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:25.292427 INFO::ASW Batch was 0.0258548889596849 prior to batch effect correction and is now -0.0899552181148939 .
2024-10-10 13:05:25.293252 INFO::Total function execution time is 0.169274091720581 s and adjustment time is 0.0637669563293457 s ( 37.67 )
2024-10-10 13:05:25.312405 INFO::Formatting Data.
2024-10-10 13:05:25.313229 INFO::Recognized SummarizedExperiment
2024-10-10 13:05:25.313654 INFO::Typecasting input to dataframe.
2024-10-10 13:05:25.322371 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:25.323519 INFO::Removing potential empty rows and columns
2024-10-10 13:05:25.326633 INFO::Found 0 missing values.
2024-10-10 13:05:25.33256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:25.333197 INFO::Done
2024-10-10 13:05:25.333663 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:25.338239 INFO::Starting hierarchical adjustment
2024-10-10 13:05:25.339096 INFO::Found 2 batches.
2024-10-10 13:05:25.339551 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:25.340064 INFO::Using default BPPARAM
2024-10-10 13:05:25.340454 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:25.341326 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:25.364051 INFO::Done
2024-10-10 13:05:25.364841 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:25.368243 INFO::ASW Batch was 0.0204306344601792 prior to batch effect correction and is now 0.0204306344601792 .
2024-10-10 13:05:25.369135 INFO::Total function execution time is 0.056765079498291 s and adjustment time is 0.0250208377838135 s ( 44.08 )
2024-10-10 13:05:25.38938 INFO::Formatting Data.
2024-10-10 13:05:25.390138 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:25.390972 INFO::Removing potential empty rows and columns
2024-10-10 13:05:25.391884 INFO::Found 0 missing values.
2024-10-10 13:05:25.394263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:25.394732 INFO::Done
2024-10-10 13:05:25.395141 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:25.396954 INFO::Starting hierarchical adjustment
2024-10-10 13:05:25.397499 INFO::Found 3 batches.
2024-10-10 13:05:25.397888 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:25.398377 INFO::Using default BPPARAM
2024-10-10 13:05:25.398774 INFO::Processing subtree level 1
2024-10-10 13:05:25.655714 INFO::Adjusting the last 1 batches sequentially
2024-10-10 13:05:25.660612 INFO::Done
2024-10-10 13:05:25.661522 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:25.666993 INFO::ASW Batch was -0.0204302799870491 prior to batch effect correction and is now -0.161677744507584 .
2024-10-10 13:05:25.669377 INFO::Total function execution time is 0.279501914978027 s and adjustment time is 0.263175964355469 s ( 94.16 )
2024-10-10 13:05:25.701059 INFO::Skipping initial DF formatting
2024-10-10 13:05:25.702428 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:25.708122 INFO::Starting hierarchical adjustment
2024-10-10 13:05:25.70923 INFO::Found 5 batches.
2024-10-10 13:05:25.709826 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:25.710675 INFO::Using default BPPARAM
2024-10-10 13:05:25.711256 INFO::Processing subtree level 1
2024-10-10 13:05:25.938476 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:25.946456 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:25.989483 INFO::Done
2024-10-10 13:05:25.990751 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:25.998577 INFO::ASW Batch was 0.481740536448399 prior to batch effect correction and is now 0.481740536448399 .
2024-10-10 13:05:25.999637 INFO::ASW Label was 0.436702933552443 prior to batch effect correction and is now 0.436702933552443 .
2024-10-10 13:05:26.006411 INFO::Total function execution time is 0.305268049240112 s and adjustment time is 0.280443906784058 s ( 91.87 )
2024-10-10 13:05:26.043022 INFO::Formatting Data.
2024-10-10 13:05:26.044468 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:26.046144 INFO::Removing potential empty rows and columns
2024-10-10 13:05:26.047942 INFO::Found 0 missing values.
2024-10-10 13:05:26.05395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:26.055578 INFO::Done
2024-10-10 13:05:26.056462 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:26.063473 INFO::Starting hierarchical adjustment
2024-10-10 13:05:26.065031 INFO::Found 5 batches.
2024-10-10 13:05:26.066004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:26.067458 INFO::Using default BPPARAM
2024-10-10 13:05:26.068335 INFO::Processing subtree level 1
2024-10-10 13:05:26.317367 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:26.321131 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:26.354199 INFO::Done
2024-10-10 13:05:26.355911 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:26.362261 INFO::ASW Batch was 0.426851236823017 prior to batch effect correction and is now -0.0825906817250055 .
2024-10-10 13:05:26.364005 INFO::ASW Label was 0.227366017142555 prior to batch effect correction and is now 0.837274828761121 .
2024-10-10 13:05:26.3654 INFO::Total function execution time is 0.32257604598999 s and adjustment time is 0.28911018371582 s ( 89.63 )
2024-10-10 13:05:26.366706 INFO::Formatting Data.
2024-10-10 13:05:26.367378 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:26.370069 INFO::Removing potential empty rows and columns
2024-10-10 13:05:26.373399 INFO::Found 0 missing values.
2024-10-10 13:05:26.379847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:26.380811 INFO::Done
2024-10-10 13:05:26.381809 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:26.387657 INFO::Starting hierarchical adjustment
2024-10-10 13:05:26.388687 INFO::Found 5 batches.
2024-10-10 13:05:26.389338 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:26.390272 INFO::Using default BPPARAM
2024-10-10 13:05:26.39093 INFO::Processing subtree level 1
2024-10-10 13:05:26.638839 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:26.643591 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:26.679483 INFO::Done
2024-10-10 13:05:26.681233 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:26.687866 INFO::ASW Batch was 0.426851236823017 prior to batch effect correction and is now -0.0825906817250055 .
2024-10-10 13:05:26.688913 INFO::ASW Label was 0.227366017142555 prior to batch effect correction and is now 0.837274828761121 .
2024-10-10 13:05:26.690256 INFO::Total function execution time is 0.323519945144653 s and adjustment time is 0.29090404510498 s ( 89.92 )
2024-10-10 13:05:26.719921 INFO::Formatting Data.
2024-10-10 13:05:26.721713 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:26.723664 INFO::Removing potential empty rows and columns
2024-10-10 13:05:26.72557 INFO::Found 0 missing values.
2024-10-10 13:05:26.731166 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:26.732092 INFO::Done
2024-10-10 13:05:26.732717 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:26.73755 INFO::Starting hierarchical adjustment
2024-10-10 13:05:26.739357 INFO::Found 5 batches.
2024-10-10 13:05:26.74009 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:26.740901 INFO::Using default BPPARAM
2024-10-10 13:05:26.741487 INFO::Processing subtree level 1
2024-10-10 13:05:26.980808 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:26.986792 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:27.022055 INFO::Done
2024-10-10 13:05:27.026446 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:27.046907 INFO::ASW Batch was 0.447473943477976 prior to batch effect correction and is now -0.0749919203000863 .
2024-10-10 13:05:27.049018 INFO::ASW Label was 0.349192560160207 prior to batch effect correction and is now 0.845183457346214 .
2024-10-10 13:05:27.054705 INFO::Total function execution time is 0.333454132080078 s and adjustment time is 0.282799005508423 s ( 84.81 )
2024-10-10 13:05:27.057991 INFO::Formatting Data.
2024-10-10 13:05:27.059303 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:27.061403 INFO::Removing potential empty rows and columns
2024-10-10 13:05:27.064243 INFO::Found 0 missing values.
2024-10-10 13:05:27.069878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:27.070965 INFO::Done
2024-10-10 13:05:27.072086 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:27.075975 INFO::Starting hierarchical adjustment
2024-10-10 13:05:27.077327 INFO::Found 5 batches.
2024-10-10 13:05:27.078142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:27.079792 INFO::Using default BPPARAM
2024-10-10 13:05:27.080613 INFO::Processing subtree level 1
2024-10-10 13:05:27.297905 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:27.302034 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:27.337319 INFO::Done
2024-10-10 13:05:27.339148 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:27.345875 INFO::ASW Batch was 0.447473943477976 prior to batch effect correction and is now -0.0749919203000863 .
2024-10-10 13:05:27.346881 INFO::ASW Label was 0.349192560160207 prior to batch effect correction and is now 0.845183457346214 .
2024-10-10 13:05:27.3483 INFO::Total function execution time is 0.290535926818848 s and adjustment time is 0.26002311706543 s ( 89.5 )
2024-10-10 13:05:27.380847 INFO::Formatting Data.
2024-10-10 13:05:27.381912 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:27.383332 INFO::Removing potential empty rows and columns
2024-10-10 13:05:27.384707 INFO::Found 0 missing values.
2024-10-10 13:05:27.389473 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:27.390544 INFO::Done
2024-10-10 13:05:27.391218 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:27.395901 INFO::Starting hierarchical adjustment
2024-10-10 13:05:27.397121 INFO::Found 2 batches.
2024-10-10 13:05:27.397909 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:27.398903 INFO::Using default BPPARAM
2024-10-10 13:05:27.399721 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:27.400896 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:27.42274 INFO::Done
2024-10-10 13:05:27.423658 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:27.42742 INFO::ASW Batch was 0.300982875527489 prior to batch effect correction and is now -0.0195249504906662 .
2024-10-10 13:05:27.428321 INFO::ASW Label was 0.760955736114022 prior to batch effect correction and is now 0.939847986435987 .
2024-10-10 13:05:27.42941 INFO::Total function execution time is 0.0487470626831055 s and adjustment time is 0.0258080959320068 s ( 52.94 )
2024-10-10 13:05:27.430344 INFO::Formatting Data.
2024-10-10 13:05:27.431149 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:27.432228 INFO::Removing potential empty rows and columns
2024-10-10 13:05:27.433453 INFO::Found 0 missing values.
2024-10-10 13:05:27.437033 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:27.437981 INFO::Done
2024-10-10 13:05:27.438656 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:27.442093 INFO::Starting hierarchical adjustment
2024-10-10 13:05:27.443044 INFO::Found 2 batches.
2024-10-10 13:05:27.443803 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:27.444824 INFO::Using default BPPARAM
2024-10-10 13:05:27.445534 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:27.446819 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:27.467906 INFO::Done
2024-10-10 13:05:27.469045 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:27.529921 INFO::ASW Batch was 0.300982875527489 prior to batch effect correction and is now -0.0195249504906662 .
2024-10-10 13:05:27.531224 INFO::ASW Label was 0.760955736114022 prior to batch effect correction and is now 0.939847986435987 .
2024-10-10 13:05:27.532627 INFO::Total function execution time is 0.102240085601807 s and adjustment time is 0.024946928024292 s ( 24.4 )
2024-10-10 13:05:27.555328 INFO::Formatting Data.
2024-10-10 13:05:27.556292 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:27.557546 INFO::Removing potential empty rows and columns
2024-10-10 13:05:27.558847 INFO::Found 0 missing values.
2024-10-10 13:05:27.562137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:27.562924 INFO::Done
2024-10-10 13:05:27.563707 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:27.568487 INFO::Starting hierarchical adjustment
2024-10-10 13:05:27.570029 INFO::Found 2 batches.
2024-10-10 13:05:27.571681 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:27.572777 INFO::Using default BPPARAM
2024-10-10 13:05:27.573683 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:27.5763 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:27.64391 INFO::Done
2024-10-10 13:05:27.645011 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:27.649789 INFO::ASW Batch was 0.110453151595849 prior to batch effect correction and is now -0.105404782645182 .
2024-10-10 13:05:27.651971 INFO::Total function execution time is 0.0965070724487305 s and adjustment time is 0.0743420124053955 s ( 77.03 )
2024-10-10 13:05:27.674487 INFO::Formatting Data.
2024-10-10 13:05:27.675735 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:27.678384 INFO::Removing potential empty rows and columns
2024-10-10 13:05:27.680644 INFO::Found 0 missing values.
2024-10-10 13:05:27.682915 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-10 13:05:27.691191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:27.692209 INFO::Done
2024-10-10 13:05:27.69304 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:27.698242 INFO::Starting hierarchical adjustment
2024-10-10 13:05:27.69928 INFO::Found 2 batches.
2024-10-10 13:05:27.700065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:27.701339 INFO::Using default BPPARAM
2024-10-10 13:05:27.702391 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:27.704042 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:27.740098 INFO::Done
2024-10-10 13:05:27.741259 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:27.746574 INFO::ASW Batch was 0.633113591149254 prior to batch effect correction and is now -0.0295400085279199 .
2024-10-10 13:05:27.747726 INFO::ASW Label was 0.449633656726777 prior to batch effect correction and is now 0.927136917577172 .
2024-10-10 13:05:27.749381 INFO::Total function execution time is 0.0749762058258057 s and adjustment time is 0.040924072265625 s ( 54.58 )
2024-10-10 13:05:27.751422 INFO::Formatting Data.
2024-10-10 13:05:27.752581 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:27.75415 INFO::Removing potential empty rows and columns
2024-10-10 13:05:27.75605 INFO::Found 0 missing values.
2024-10-10 13:05:27.757632 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-10 13:05:27.771243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:27.773134 INFO::Done
2024-10-10 13:05:27.774274 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:27.778213 INFO::Starting hierarchical adjustment
2024-10-10 13:05:27.779261 INFO::Found 2 batches.
2024-10-10 13:05:27.779826 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:27.780695 INFO::Using default BPPARAM
2024-10-10 13:05:27.781309 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:27.782921 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:27.81886 INFO::Done
2024-10-10 13:05:27.820029 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:27.82621 INFO::ASW Batch was 0.633113591149254 prior to batch effect correction and is now -0.0295400085279199 .
2024-10-10 13:05:27.827197 INFO::ASW Label was 0.449633656726777 prior to batch effect correction and is now 0.927136917577172 .
2024-10-10 13:05:27.828176 INFO::Total function execution time is 0.0770149230957031 s and adjustment time is 0.0396912097930908 s ( 51.54 )
2024-10-10 13:05:28.190981 INFO::Formatting Data.
2024-10-10 13:05:28.192679 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:28.193602 INFO::Removing potential empty rows and columns
2024-10-10 13:05:28.194693 INFO::Found 0 missing values.
2024-10-10 13:05:28.199775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:28.202492 INFO::Done
2024-10-10 13:05:28.203753 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:28.206856 INFO::Starting hierarchical adjustment
2024-10-10 13:05:28.207811 INFO::Found 3 batches.
2024-10-10 13:05:28.209457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:28.210095 INFO::Using default BPPARAM
2024-10-10 13:05:28.210768 INFO::Processing subtree level 1
2024-10-10 13:05:28.43291 INFO::Adjusting the last 1 batches sequentially
2024-10-10 13:05:28.436902 INFO::Done
2024-10-10 13:05:28.437646 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:28.442846 INFO::ASW Batch was -0.0742133115935796 prior to batch effect correction and is now -0.0742133115935796 .
2024-10-10 13:05:28.446055 INFO::Total function execution time is 0.254331827163696 s and adjustment time is 0.229317188262939 s ( 90.16 )
2024-10-10 13:05:28.447518 INFO::Formatting Data.
2024-10-10 13:05:28.448274 INFO::Typecasting input to dataframe.
2024-10-10 13:05:28.449059 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:28.450244 INFO::Removing potential empty rows and columns
2024-10-10 13:05:28.451613 INFO::Found 0 missing values.
2024-10-10 13:05:28.455747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:28.456547 INFO::Done
2024-10-10 13:05:28.457341 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:28.459903 INFO::Starting hierarchical adjustment
2024-10-10 13:05:28.460794 INFO::Found 3 batches.
2024-10-10 13:05:28.461585 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:28.462633 INFO::Using default BPPARAM
2024-10-10 13:05:28.463618 INFO::Processing subtree level 1
2024-10-10 13:05:28.642491 INFO::Adjusting the last 1 batches sequentially
2024-10-10 13:05:28.647875 INFO::Done
2024-10-10 13:05:28.648787 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:28.654378 INFO::ASW Batch was -0.0742133115935796 prior to batch effect correction and is now -0.0742133115935796 .
2024-10-10 13:05:28.65757 INFO::Total function execution time is 0.20947003364563 s and adjustment time is 0.187227010726929 s ( 89.38 )
2024-10-10 13:05:28.685635 INFO::Formatting Data.
2024-10-10 13:05:28.686629 INFO::Typecasting input to dataframe.
2024-10-10 13:05:28.687619 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:28.688727 INFO::Removing potential empty rows and columns
2024-10-10 13:05:28.690222 INFO::Found 0 missing values.
2024-10-10 13:05:28.693817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:28.694652 INFO::Done
2024-10-10 13:05:28.695319 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:28.697903 INFO::Starting hierarchical adjustment
2024-10-10 13:05:28.698789 INFO::Found 3 batches.
2024-10-10 13:05:28.69934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:28.700144 INFO::Using default BPPARAM
2024-10-10 13:05:28.700668 INFO::Processing subtree level 1
2024-10-10 13:05:28.880396 INFO::Adjusting the last 1 batches sequentially
2024-10-10 13:05:28.88504 INFO::Done
2024-10-10 13:05:28.885806 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:28.890887 INFO::ASW Batch was -0.0498820803705732 prior to batch effect correction and is now -0.0498820803705732 .
2024-10-10 13:05:28.892333 INFO::Total function execution time is 0.2067711353302 s and adjustment time is 0.186428070068359 s ( 90.16 )
2024-10-10 13:05:29.173466 INFO::Formatting Data.
2024-10-10 13:05:29.17902 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:29.181183 INFO::Removing potential empty rows and columns
2024-10-10 13:05:29.185033 INFO::Found 1000 missing values.
2024-10-10 13:05:29.214283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:29.215798 INFO::Done
2024-10-10 13:05:29.216409 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:29.224914 INFO::Starting hierarchical adjustment
2024-10-10 13:05:29.228185 INFO::Found 10 batches.
2024-10-10 13:05:29.229057 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:29.229982 INFO::Using default BPPARAM
2024-10-10 13:05:29.230548 INFO::Processing subtree level 1
2024-10-10 13:05:29.62216 INFO::Processing subtree level 2
2024-10-10 13:05:29.999714 INFO::Adjusting the last 1 batches sequentially
2024-10-10 13:05:30.006439 INFO::Done
2024-10-10 13:05:30.007475 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:30.019455 INFO::ASW Batch was 0.503608200080148 prior to batch effect correction and is now 0.503608200080147 .
2024-10-10 13:05:30.020482 INFO::ASW Label was 0.367704798630092 prior to batch effect correction and is now 0.367704798630092 .
2024-10-10 13:05:30.022307 INFO::Total function execution time is 0.848871946334839 s and adjustment time is 0.780061960220337 s ( 91.89 )
2024-10-10 13:05:30.023771 INFO::Formatting Data.
2024-10-10 13:05:30.02706 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:30.029556 INFO::Removing potential empty rows and columns
2024-10-10 13:05:30.036458 INFO::Found 1000 missing values.
2024-10-10 13:05:30.080773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:30.08176 INFO::Done
2024-10-10 13:05:30.082548 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:30.091746 INFO::Starting hierarchical adjustment
2024-10-10 13:05:30.093872 INFO::Found 10 batches.
2024-10-10 13:05:31.620502 INFO::Set up parallel execution backend with 2 workers
2024-10-10 13:05:31.621421 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-10 13:05:33.250168 INFO::Adjusting the last 2 batches sequentially
2024-10-10 13:05:33.251789 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-10 13:05:33.272382 INFO::Done
2024-10-10 13:05:33.273652 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:33.28133 INFO::ASW Batch was 0.503608200080148 prior to batch effect correction and is now 0.503608200080147 .
2024-10-10 13:05:33.282271 INFO::ASW Label was 0.367704798630092 prior to batch effect correction and is now 0.367704798630092 .
2024-10-10 13:05:33.28343 INFO::Total function execution time is 3.25982189178467 s and adjustment time is 3.17890906333923 s ( 97.52 )
2024-10-10 13:05:33.561626 INFO::Formatting Data.
2024-10-10 13:05:33.562802 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:33.564065 INFO::Removing potential empty rows and columns
2024-10-10 13:05:33.565445 INFO::Found 0 missing values.
2024-10-10 13:05:33.570044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:33.570818 INFO::Done
2024-10-10 13:05:33.571483 INFO::Acquiring quality metrics before batch effect correction.
2024-10-10 13:05:33.574978 INFO::Starting hierarchical adjustment
2024-10-10 13:05:33.575865 INFO::Found 3 batches.
2024-10-10 13:05:33.576429 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-10 13:05:33.577577 INFO::Using default BPPARAM
2024-10-10 13:05:33.578721 INFO::Processing subtree level 1
2024-10-10 13:05:33.777713 INFO::Adjusting the last 1 batches sequentially
2024-10-10 13:05:33.782508 INFO::Done
2024-10-10 13:05:33.783337 INFO::Acquiring quality metrics after batch effect correction.
2024-10-10 13:05:33.792491 INFO::ASW Batch was 0.218675940429407 prior to batch effect correction and is now -0.134248839352003 .
2024-10-10 13:05:33.793671 INFO::ASW Label was -0.198475747627781 prior to batch effect correction and is now -0.0495462506440849 .
2024-10-10 13:05:33.796247 INFO::Total function execution time is 0.234019041061401 s and adjustment time is 0.206824064254761 s ( 88.38 )
2024-10-10 13:05:33.98099 INFO::Formatting Data.
2024-10-10 13:05:33.981953 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:33.982965 INFO::Removing potential empty rows and columns
2024-10-10 13:05:33.984057 INFO::Found 2 missing values.
2024-10-10 13:05:33.987948 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:33.989038 INFO::Done
2024-10-10 13:05:34.03113 INFO::Found NA in Reference column
2024-10-10 13:05:34.046585 INFO::Require at least two references per batch.
2024-10-10 13:05:34.083583 INFO::Formatting Data.
2024-10-10 13:05:34.086188 INFO::Recognized SummarizedExperiment
2024-10-10 13:05:34.087425 INFO::Typecasting input to dataframe.
2024-10-10 13:05:34.103822 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:34.105494 INFO::Removing potential empty rows and columns
2024-10-10 13:05:34.11514 INFO::Found 0 missing values.
2024-10-10 13:05:34.123992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:34.124856 INFO::Done
2024-10-10 13:05:34.148153 INFO::Formatting Data.
2024-10-10 13:05:34.150557 INFO::Recognized SummarizedExperiment
2024-10-10 13:05:34.151625 INFO::Typecasting input to dataframe.
2024-10-10 13:05:34.183785 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:34.186347 INFO::Removing potential empty rows and columns
2024-10-10 13:05:34.191332 INFO::Found 0 missing values.
2024-10-10 13:05:34.209121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:34.210538 INFO::Done
2024-10-10 13:05:34.234487 INFO::Formatting Data.
2024-10-10 13:05:34.235541 INFO::Recognized SummarizedExperiment
2024-10-10 13:05:34.238738 INFO::Typecasting input to dataframe.
2024-10-10 13:05:34.273023 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:34.274718 INFO::Removing potential empty rows and columns
2024-10-10 13:05:34.2761 INFO::Found 0 missing values.
2024-10-10 13:05:34.277289 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-10 13:05:34.284794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:34.285704 INFO::Done
2024-10-10 13:05:34.30651 INFO::Formatting Data.
2024-10-10 13:05:34.307601 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:34.308594 INFO::Removing potential empty rows and columns
2024-10-10 13:05:34.309682 INFO::Found 0 missing values.
2024-10-10 13:05:34.315335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:34.316214 INFO::Done
2024-10-10 13:05:34.341973 INFO::Formatting Data.
2024-10-10 13:05:34.342918 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:34.344256 INFO::Removing potential empty rows and columns
2024-10-10 13:05:34.348259 INFO::Found 0 missing values.
2024-10-10 13:05:34.352774 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:34.353645 INFO::Done
2024-10-10 13:05:34.393572 INFO::Formatting Data.
2024-10-10 13:05:34.394563 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:34.397034 INFO::Removing potential empty rows and columns
2024-10-10 13:05:34.398952 INFO::Found 1 missing values.
2024-10-10 13:05:34.402243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:34.402978 INFO::Done
2024-10-10 13:05:34.434487 INFO::Formatting Data.
2024-10-10 13:05:34.435695 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:34.436806 INFO::Removing potential empty rows and columns
2024-10-10 13:05:34.437905 INFO::Found 2 missing values.
2024-10-10 13:05:34.439046 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-10-10 13:05:34.441944 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:34.442658 INFO::Done
2024-10-10 13:05:34.464351 INFO::Formatting Data.
2024-10-10 13:05:34.469002 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:34.470243 INFO::Removing potential empty rows and columns
2024-10-10 13:05:34.471457 INFO::Found 2 missing values.
2024-10-10 13:05:34.473289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:34.473945 INFO::Done
2024-10-10 13:05:34.491943 INFO::Formatting Data.
2024-10-10 13:05:34.492905 INFO::Typecasting input to dataframe.
2024-10-10 13:05:34.493809 INFO::Replacing NaNs with NAs.
2024-10-10 13:05:34.494788 INFO::Removing potential empty rows and columns
2024-10-10 13:05:34.495961 INFO::Found 0 missing values.
2024-10-10 13:05:34.499809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-10 13:05:34.50049 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.627 6.689 28.756
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 30.330 | 1.549 | 23.341 | |
| compute_asw | 0.031 | 0.002 | 0.033 | |
| count_existing | 0.016 | 0.001 | 0.018 | |
| generate_data_covariables | 0.016 | 0.001 | 0.017 | |
| generate_dataset | 0.016 | 0.001 | 0.016 | |