Yannis Schumann
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 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 2024-10-18 20:38 -0400 (Fri, 18 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" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-10-16 21:56:27 -0400 (Wed, 16 Oct 2024) |
| EndedAt: 2024-10-16 21:57:55 -0400 (Wed, 16 Oct 2024) |
| EllapsedTime: 88.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 24.876 1.579 18.31
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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: x86_64-pc-linux-gnu
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")
2024-10-16 21:57:19.28616 INFO::Formatting Data.
2024-10-16 21:57:19.287732 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:19.298806 INFO::Removing potential empty rows and columns
2024-10-16 21:57:19.535018 INFO::Found 0 missing values.
2024-10-16 21:57:19.538106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:19.538665 INFO::Done
2024-10-16 21:57:19.539161 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:19.550026 INFO::Starting hierarchical adjustment
2024-10-16 21:57:19.55077 INFO::Found 3 batches.
2024-10-16 21:57:19.551298 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:19.552294 INFO::Using default BPPARAM
2024-10-16 21:57:19.552796 INFO::Processing subtree level 1
2024-10-16 21:57:19.641902 INFO::Adjusting the last 1 batches sequentially
2024-10-16 21:57:19.643594 INFO::Done
2024-10-16 21:57:19.644227 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:19.646646 INFO::ASW Batch was 0.0170171912828257 prior to batch effect correction and is now 0.0170171912828257 .
2024-10-16 21:57:19.647736 INFO::Total function execution time is 0.362438678741455 s and adjustment time is 0.0929701328277588 s ( 25.65 )
2024-10-16 21:57:19.660255 INFO::Formatting Data.
2024-10-16 21:57:19.660953 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:19.661782 INFO::Removing potential empty rows and columns
2024-10-16 21:57:19.662751 INFO::Found 0 missing values.
2024-10-16 21:57:19.663676 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.
2024-10-16 21:57:19.67347 INFO::Formatting Data.
2024-10-16 21:57:19.674098 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:19.674881 INFO::Removing potential empty rows and columns
2024-10-16 21:57:19.675843 INFO::Found 0 missing values.
2024-10-16 21:57:19.676664 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.
2024-10-16 21:57:19.690727 INFO::Formatting Data.
2024-10-16 21:57:19.691417 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:19.6922 INFO::Removing potential empty rows and columns
2024-10-16 21:57:19.693139 INFO::Found 0 missing values.
2024-10-16 21:57:19.693973 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.
2024-10-16 21:57:19.698427 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:19.698977 INFO::Done
2024-10-16 21:57:19.699489 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:19.701538 INFO::Starting hierarchical adjustment
2024-10-16 21:57:19.702198 INFO::Found 2 batches.
2024-10-16 21:57:19.702724 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:19.703374 INFO::Using default BPPARAM
2024-10-16 21:57:19.703888 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:19.704774 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:19.726543 INFO::Done
2024-10-16 21:57:19.727223 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:19.729141 INFO::ASW Batch was -0.0110404830295886 prior to batch effect correction and is now -0.130534250948562 .
2024-10-16 21:57:19.729912 INFO::Total function execution time is 0.0392262935638428 s and adjustment time is 0.024463415145874 s ( 62.36 )
2024-10-16 21:57:19.732677 INFO::Formatting Data.
2024-10-16 21:57:19.733286 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:19.741731 INFO::Formatting Data.
2024-10-16 21:57:19.742411 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:19.743299 INFO::Removing potential empty rows and columns
2024-10-16 21:57:19.744328 INFO::Found 0 missing values.
2024-10-16 21:57:19.747454 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:19.748057 INFO::Done
2024-10-16 21:57:19.748572 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:19.750565 INFO::Starting hierarchical adjustment
2024-10-16 21:57:19.751281 INFO::Found 2 batches.
2024-10-16 21:57:19.751801 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:19.752392 INFO::Using default BPPARAM
2024-10-16 21:57:19.752911 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:19.753817 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:19.768184 INFO::Done
2024-10-16 21:57:19.7688 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:19.77068 INFO::ASW Batch was 0.0729762844833894 prior to batch effect correction and is now -0.124669606714592 .
2024-10-16 21:57:19.771425 INFO::Total function execution time is 0.0297186374664307 s and adjustment time is 0.0170700550079346 s ( 57.44 )
2024-10-16 21:57:19.772439 INFO::Formatting Data.
2024-10-16 21:57:19.773023 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:19.773818 INFO::Removing potential empty rows and columns
2024-10-16 21:57:19.774775 INFO::Found 0 missing values.
2024-10-16 21:57:19.777471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:19.777975 INFO::Done
2024-10-16 21:57:19.778467 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:19.780389 INFO::Starting hierarchical adjustment
2024-10-16 21:57:19.781045 INFO::Found 2 batches.
2024-10-16 21:57:19.781535 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:19.782093 INFO::Using default BPPARAM
2024-10-16 21:57:19.782592 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:19.783435 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:19.797591 INFO::Done
2024-10-16 21:57:19.798231 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:19.800158 INFO::ASW Batch was 0.0729762844833894 prior to batch effect correction and is now -0.124669606714592 .
2024-10-16 21:57:19.800904 INFO::Total function execution time is 0.0284557342529297 s and adjustment time is 0.016676664352417 s ( 58.61 )
2024-10-16 21:57:21.803124 INFO::Formatting Data.
2024-10-16 21:57:21.803809 INFO::Recognized SummarizedExperiment
2024-10-16 21:57:21.804299 INFO::Typecasting input to dataframe.
2024-10-16 21:57:21.856409 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:21.857482 INFO::Removing potential empty rows and columns
2024-10-16 21:57:21.860421 INFO::Found 0 missing values.
2024-10-16 21:57:21.86588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:21.866343 INFO::Done
2024-10-16 21:57:21.866775 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:21.869528 INFO::Starting hierarchical adjustment
2024-10-16 21:57:21.87011 INFO::Found 2 batches.
2024-10-16 21:57:21.870537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:21.871397 INFO::Using default BPPARAM
2024-10-16 21:57:21.87183 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:21.872644 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:21.915198 INFO::Done
2024-10-16 21:57:21.9158 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:21.918612 INFO::ASW Batch was 0.00476944675218065 prior to batch effect correction and is now -0.0889759561946818 .
2024-10-16 21:57:21.919294 INFO::Total function execution time is 0.116466999053955 s and adjustment time is 0.0451931953430176 s ( 38.8 )
2024-10-16 21:57:21.933225 INFO::Formatting Data.
2024-10-16 21:57:21.933788 INFO::Recognized SummarizedExperiment
2024-10-16 21:57:21.934224 INFO::Typecasting input to dataframe.
2024-10-16 21:57:21.941653 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:21.942603 INFO::Removing potential empty rows and columns
2024-10-16 21:57:21.945375 INFO::Found 0 missing values.
2024-10-16 21:57:21.950787 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:21.951285 INFO::Done
2024-10-16 21:57:21.951743 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:21.954654 INFO::Starting hierarchical adjustment
2024-10-16 21:57:21.955295 INFO::Found 2 batches.
2024-10-16 21:57:21.955739 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:21.956245 INFO::Using default BPPARAM
2024-10-16 21:57:21.956682 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:21.957522 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:21.976973 INFO::Done
2024-10-16 21:57:21.977581 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:21.980525 INFO::ASW Batch was -0.00106540567033626 prior to batch effect correction and is now -0.00106540567033626 .
2024-10-16 21:57:21.981281 INFO::Total function execution time is 0.0480103492736816 s and adjustment time is 0.0217914581298828 s ( 45.39 )
2024-10-16 21:57:21.99607 INFO::Formatting Data.
2024-10-16 21:57:21.996732 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:21.997479 INFO::Removing potential empty rows and columns
2024-10-16 21:57:21.998318 INFO::Found 0 missing values.
2024-10-16 21:57:22.000728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:22.00118 INFO::Done
2024-10-16 21:57:22.001607 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:22.00327 INFO::Starting hierarchical adjustment
2024-10-16 21:57:22.003867 INFO::Found 3 batches.
2024-10-16 21:57:22.004351 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:22.004878 INFO::Using default BPPARAM
2024-10-16 21:57:22.005337 INFO::Processing subtree level 1
2024-10-16 21:57:22.159983 INFO::Adjusting the last 1 batches sequentially
2024-10-16 21:57:22.162742 INFO::Done
2024-10-16 21:57:22.163498 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:22.166428 INFO::ASW Batch was -0.123051910385079 prior to batch effect correction and is now -0.179550864987656 .
2024-10-16 21:57:22.167624 INFO::Total function execution time is 0.171501636505127 s and adjustment time is 0.158946990966797 s ( 92.68 )
2024-10-16 21:57:22.186466 INFO::Skipping initial DF formatting
2024-10-16 21:57:22.187526 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:22.192542 INFO::Starting hierarchical adjustment
2024-10-16 21:57:22.193874 INFO::Found 5 batches.
2024-10-16 21:57:22.194665 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:22.195467 INFO::Using default BPPARAM
2024-10-16 21:57:22.196041 INFO::Processing subtree level 1
2024-10-16 21:57:22.333965 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:22.335551 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:22.354802 INFO::Done
2024-10-16 21:57:22.355493 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:22.35933 INFO::ASW Batch was 0.481770143508943 prior to batch effect correction and is now 0.481770143508943 .
2024-10-16 21:57:22.359939 INFO::ASW Label was 0.424546954354144 prior to batch effect correction and is now 0.424546954354144 .
2024-10-16 21:57:22.360721 INFO::Total function execution time is 0.174463272094727 s and adjustment time is 0.161286115646362 s ( 92.45 )
2024-10-16 21:57:22.37679 INFO::Formatting Data.
2024-10-16 21:57:22.377597 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:22.378502 INFO::Removing potential empty rows and columns
2024-10-16 21:57:22.379468 INFO::Found 0 missing values.
2024-10-16 21:57:22.383478 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:22.383994 INFO::Done
2024-10-16 21:57:22.384507 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:22.387283 INFO::Starting hierarchical adjustment
2024-10-16 21:57:22.387931 INFO::Found 5 batches.
2024-10-16 21:57:22.388422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:22.389012 INFO::Using default BPPARAM
2024-10-16 21:57:22.389517 INFO::Processing subtree level 1
2024-10-16 21:57:22.4978 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:22.49932 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:22.514426 INFO::Done
2024-10-16 21:57:22.515157 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:22.518196 INFO::ASW Batch was 0.455859115076425 prior to batch effect correction and is now -0.0979100045709327 .
2024-10-16 21:57:22.518802 INFO::ASW Label was 0.246056904332966 prior to batch effect correction and is now 0.893272740129216 .
2024-10-16 21:57:22.519595 INFO::Total function execution time is 0.142862319946289 s and adjustment time is 0.126603364944458 s ( 88.62 )
2024-10-16 21:57:22.520388 INFO::Formatting Data.
2024-10-16 21:57:22.520985 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:22.521807 INFO::Removing potential empty rows and columns
2024-10-16 21:57:22.522729 INFO::Found 0 missing values.
2024-10-16 21:57:22.526544 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:22.527073 INFO::Done
2024-10-16 21:57:22.527572 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:22.53037 INFO::Starting hierarchical adjustment
2024-10-16 21:57:22.531059 INFO::Found 5 batches.
2024-10-16 21:57:22.531571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:22.532173 INFO::Using default BPPARAM
2024-10-16 21:57:22.532744 INFO::Processing subtree level 1
2024-10-16 21:57:22.638027 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:22.639561 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:22.654022 INFO::Done
2024-10-16 21:57:22.654658 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:22.6576 INFO::ASW Batch was 0.455859115076425 prior to batch effect correction and is now -0.0979100045709327 .
2024-10-16 21:57:22.658172 INFO::ASW Label was 0.246056904332966 prior to batch effect correction and is now 0.893272740129216 .
2024-10-16 21:57:22.658924 INFO::Total function execution time is 0.138532876968384 s and adjustment time is 0.123101234436035 s ( 88.86 )
2024-10-16 21:57:22.670508 INFO::Formatting Data.
2024-10-16 21:57:22.671185 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:22.672027 INFO::Removing potential empty rows and columns
2024-10-16 21:57:22.672934 INFO::Found 0 missing values.
2024-10-16 21:57:22.676569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:22.677054 INFO::Done
2024-10-16 21:57:22.677525 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:22.680236 INFO::Starting hierarchical adjustment
2024-10-16 21:57:22.680887 INFO::Found 5 batches.
2024-10-16 21:57:22.681374 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:22.681958 INFO::Using default BPPARAM
2024-10-16 21:57:22.682443 INFO::Processing subtree level 1
2024-10-16 21:57:22.795202 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:22.797035 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:22.813786 INFO::Done
2024-10-16 21:57:22.814639 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:22.81829 INFO::ASW Batch was 0.230101235363922 prior to batch effect correction and is now -0.0109640077999234 .
2024-10-16 21:57:22.819018 INFO::ASW Label was 0.490704015763086 prior to batch effect correction and is now 0.763453927955847 .
2024-10-16 21:57:22.819966 INFO::Total function execution time is 0.14943528175354 s and adjustment time is 0.132974863052368 s ( 88.98 )
2024-10-16 21:57:22.820882 INFO::Formatting Data.
2024-10-16 21:57:22.821559 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:22.822514 INFO::Removing potential empty rows and columns
2024-10-16 21:57:22.823538 INFO::Found 0 missing values.
2024-10-16 21:57:22.827688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:22.828237 INFO::Done
2024-10-16 21:57:22.82877 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:22.832027 INFO::Starting hierarchical adjustment
2024-10-16 21:57:22.832739 INFO::Found 5 batches.
2024-10-16 21:57:22.833305 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:22.833959 INFO::Using default BPPARAM
2024-10-16 21:57:22.834474 INFO::Processing subtree level 1
2024-10-16 21:57:22.959959 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:22.961782 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:22.977715 INFO::Done
2024-10-16 21:57:22.978505 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:22.981993 INFO::ASW Batch was 0.230101235363922 prior to batch effect correction and is now -0.0109640077999234 .
2024-10-16 21:57:22.982667 INFO::ASW Label was 0.490704015763086 prior to batch effect correction and is now 0.763453927955847 .
2024-10-16 21:57:22.983546 INFO::Total function execution time is 0.162671566009521 s and adjustment time is 0.145086765289307 s ( 89.19 )
2024-10-16 21:57:22.996545 INFO::Formatting Data.
2024-10-16 21:57:22.997251 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:22.998159 INFO::Removing potential empty rows and columns
2024-10-16 21:57:22.999226 INFO::Found 0 missing values.
2024-10-16 21:57:23.002044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:23.002588 INFO::Done
2024-10-16 21:57:23.003129 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:23.006193 INFO::Starting hierarchical adjustment
2024-10-16 21:57:23.006942 INFO::Found 2 batches.
2024-10-16 21:57:23.007472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:23.008113 INFO::Using default BPPARAM
2024-10-16 21:57:23.008634 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:23.00957 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:23.023755 INFO::Done
2024-10-16 21:57:23.0244 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:23.027411 INFO::ASW Batch was 0.615383378039533 prior to batch effect correction and is now -0.0269201046807711 .
2024-10-16 21:57:23.028004 INFO::ASW Label was 0.41321740483743 prior to batch effect correction and is now 0.922702708736597 .
2024-10-16 21:57:23.028821 INFO::Total function execution time is 0.0323429107666016 s and adjustment time is 0.0169789791107178 s ( 52.5 )
2024-10-16 21:57:23.029675 INFO::Formatting Data.
2024-10-16 21:57:23.030324 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:23.031229 INFO::Removing potential empty rows and columns
2024-10-16 21:57:23.032243 INFO::Found 0 missing values.
2024-10-16 21:57:23.034926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:23.035489 INFO::Done
2024-10-16 21:57:23.036002 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:23.038842 INFO::Starting hierarchical adjustment
2024-10-16 21:57:23.039559 INFO::Found 2 batches.
2024-10-16 21:57:23.04007 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:23.040674 INFO::Using default BPPARAM
2024-10-16 21:57:23.041203 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:23.042129 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:23.056596 INFO::Done
2024-10-16 21:57:23.057151 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:23.075462 INFO::ASW Batch was 0.615383378039533 prior to batch effect correction and is now -0.0269201046807711 .
2024-10-16 21:57:23.076048 INFO::ASW Label was 0.41321740483743 prior to batch effect correction and is now 0.922702708736597 .
2024-10-16 21:57:23.076816 INFO::Total function execution time is 0.0471882820129395 s and adjustment time is 0.0171856880187988 s ( 36.42 )
2024-10-16 21:57:23.087089 INFO::Formatting Data.
2024-10-16 21:57:23.087717 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:23.088531 INFO::Removing potential empty rows and columns
2024-10-16 21:57:23.089434 INFO::Found 0 missing values.
2024-10-16 21:57:23.091577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:23.092115 INFO::Done
2024-10-16 21:57:23.092615 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:23.09446 INFO::Starting hierarchical adjustment
2024-10-16 21:57:23.095169 INFO::Found 2 batches.
2024-10-16 21:57:23.095702 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:23.096272 INFO::Using default BPPARAM
2024-10-16 21:57:23.096801 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:23.097675 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:23.128725 INFO::Done
2024-10-16 21:57:23.12938 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:23.131263 INFO::ASW Batch was 0.076155898212556 prior to batch effect correction and is now -0.093825082171127 .
2024-10-16 21:57:23.13205 INFO::Total function execution time is 0.0449695587158203 s and adjustment time is 0.0336785316467285 s ( 74.89 )
2024-10-16 21:57:23.14364 INFO::Formatting Data.
2024-10-16 21:57:23.144334 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:23.145176 INFO::Removing potential empty rows and columns
2024-10-16 21:57:23.14619 INFO::Found 0 missing values.
2024-10-16 21:57:23.147388 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.
2024-10-16 21:57:23.152236 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:23.152823 INFO::Done
2024-10-16 21:57:23.153352 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:23.156438 INFO::Starting hierarchical adjustment
2024-10-16 21:57:23.15712 INFO::Found 2 batches.
2024-10-16 21:57:23.157648 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:23.158251 INFO::Using default BPPARAM
2024-10-16 21:57:23.158785 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:23.159808 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:23.176693 INFO::Done
2024-10-16 21:57:23.177299 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:23.180188 INFO::ASW Batch was 0.391438668411785 prior to batch effect correction and is now 0.311466869448313 .
2024-10-16 21:57:23.180793 INFO::ASW Label was 0.694083941546038 prior to batch effect correction and is now 0.752746988756476 .
2024-10-16 21:57:23.181511 INFO::Total function execution time is 0.0379345417022705 s and adjustment time is 0.0197255611419678 s ( 52 )
2024-10-16 21:57:23.182281 INFO::Formatting Data.
2024-10-16 21:57:23.182864 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:23.183739 INFO::Removing potential empty rows and columns
2024-10-16 21:57:23.184662 INFO::Found 0 missing values.
2024-10-16 21:57:23.185491 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.
2024-10-16 21:57:23.189747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:23.190252 INFO::Done
2024-10-16 21:57:23.190731 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:23.193426 INFO::Starting hierarchical adjustment
2024-10-16 21:57:23.194084 INFO::Found 2 batches.
2024-10-16 21:57:23.194593 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:23.195212 INFO::Using default BPPARAM
2024-10-16 21:57:23.195757 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:23.19662 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:23.212786 INFO::Done
2024-10-16 21:57:23.213415 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:23.216256 INFO::ASW Batch was 0.391438668411785 prior to batch effect correction and is now 0.311466869448313 .
2024-10-16 21:57:23.216821 INFO::ASW Label was 0.694083941546038 prior to batch effect correction and is now 0.752746988756476 .
2024-10-16 21:57:23.217588 INFO::Total function execution time is 0.0353183746337891 s and adjustment time is 0.0188512802124023 s ( 53.38 )
2024-10-16 21:57:23.419093 INFO::Formatting Data.
2024-10-16 21:57:23.419939 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:23.420858 INFO::Removing potential empty rows and columns
2024-10-16 21:57:23.421885 INFO::Found 0 missing values.
2024-10-16 21:57:23.424948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:23.425493 INFO::Done
2024-10-16 21:57:23.426018 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:23.428073 INFO::Starting hierarchical adjustment
2024-10-16 21:57:23.428783 INFO::Found 3 batches.
2024-10-16 21:57:23.429311 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:23.429903 INFO::Using default BPPARAM
2024-10-16 21:57:23.430444 INFO::Processing subtree level 1
2024-10-16 21:57:23.53903 INFO::Adjusting the last 1 batches sequentially
2024-10-16 21:57:23.540935 INFO::Done
2024-10-16 21:57:23.541629 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:23.544321 INFO::ASW Batch was -0.120720353157809 prior to batch effect correction and is now -0.120720353157809 .
2024-10-16 21:57:23.545323 INFO::Total function execution time is 0.126305103302002 s and adjustment time is 0.112253904342651 s ( 88.88 )
2024-10-16 21:57:23.546491 INFO::Formatting Data.
2024-10-16 21:57:23.547177 INFO::Typecasting input to dataframe.
2024-10-16 21:57:23.54794 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:23.548934 INFO::Removing potential empty rows and columns
2024-10-16 21:57:23.550022 INFO::Found 0 missing values.
2024-10-16 21:57:23.553214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:23.553816 INFO::Done
2024-10-16 21:57:23.554403 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:23.556586 INFO::Starting hierarchical adjustment
2024-10-16 21:57:23.55733 INFO::Found 3 batches.
2024-10-16 21:57:23.557827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:23.55843 INFO::Using default BPPARAM
2024-10-16 21:57:23.558963 INFO::Processing subtree level 1
2024-10-16 21:57:23.658253 INFO::Adjusting the last 1 batches sequentially
2024-10-16 21:57:23.660172 INFO::Done
2024-10-16 21:57:23.660839 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:23.663505 INFO::ASW Batch was -0.120720353157809 prior to batch effect correction and is now -0.120720353157809 .
2024-10-16 21:57:23.664545 INFO::Total function execution time is 0.118023633956909 s and adjustment time is 0.102967262268066 s ( 87.24 )
2024-10-16 21:57:23.677359 INFO::Formatting Data.
2024-10-16 21:57:23.678166 INFO::Typecasting input to dataframe.
2024-10-16 21:57:23.679135 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:23.680131 INFO::Removing potential empty rows and columns
2024-10-16 21:57:23.681288 INFO::Found 0 missing values.
2024-10-16 21:57:23.684475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:23.68504 INFO::Done
2024-10-16 21:57:23.685611 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:23.687667 INFO::Starting hierarchical adjustment
2024-10-16 21:57:23.688418 INFO::Found 3 batches.
2024-10-16 21:57:23.688962 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:23.689571 INFO::Using default BPPARAM
2024-10-16 21:57:23.690099 INFO::Processing subtree level 1
2024-10-16 21:57:23.782643 INFO::Adjusting the last 1 batches sequentially
2024-10-16 21:57:23.784575 INFO::Done
2024-10-16 21:57:23.785264 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:23.787964 INFO::ASW Batch was 0.0385695899679006 prior to batch effect correction and is now 0.0385695899679006 .
2024-10-16 21:57:23.788987 INFO::Total function execution time is 0.111657619476318 s and adjustment time is 0.0962650775909424 s ( 86.21 )
2024-10-16 21:57:23.939394 INFO::Formatting Data.
2024-10-16 21:57:23.940341 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:23.941916 INFO::Removing potential empty rows and columns
2024-10-16 21:57:23.945284 INFO::Found 1000 missing values.
2024-10-16 21:57:23.97072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:23.971681 INFO::Done
2024-10-16 21:57:23.972535 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:23.980438 INFO::Starting hierarchical adjustment
2024-10-16 21:57:23.981441 INFO::Found 10 batches.
2024-10-16 21:57:23.982132 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:23.983125 INFO::Using default BPPARAM
2024-10-16 21:57:23.983701 INFO::Processing subtree level 1
2024-10-16 21:57:24.239651 INFO::Processing subtree level 2
2024-10-16 21:57:24.436938 INFO::Adjusting the last 1 batches sequentially
2024-10-16 21:57:24.439189 INFO::Done
2024-10-16 21:57:24.439933 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:24.446376 INFO::ASW Batch was 0.536574470817458 prior to batch effect correction and is now 0.536574470817458 .
2024-10-16 21:57:24.447086 INFO::ASW Label was 0.327149097613058 prior to batch effect correction and is now 0.327149097613058 .
2024-10-16 21:57:24.448142 INFO::Total function execution time is 0.508867263793945 s and adjustment time is 0.457886695861816 s ( 89.98 )
2024-10-16 21:57:24.449086 INFO::Formatting Data.
2024-10-16 21:57:24.449779 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:24.451312 INFO::Removing potential empty rows and columns
2024-10-16 21:57:24.454801 INFO::Found 1000 missing values.
2024-10-16 21:57:24.476583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:24.477468 INFO::Done
2024-10-16 21:57:24.478101 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:24.483999 INFO::Starting hierarchical adjustment
2024-10-16 21:57:24.48477 INFO::Found 10 batches.
2024-10-16 21:57:25.662272 INFO::Set up parallel execution backend with 2 workers
2024-10-16 21:57:25.667181 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-16 21:57:26.727597 INFO::Adjusting the last 2 batches sequentially
2024-10-16 21:57:26.729225 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 21:57:26.745189 INFO::Done
2024-10-16 21:57:26.745791 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:26.750475 INFO::ASW Batch was 0.536574470817458 prior to batch effect correction and is now 0.536574470817458 .
2024-10-16 21:57:26.751027 INFO::ASW Label was 0.327149097613058 prior to batch effect correction and is now 0.327149097613058 .
2024-10-16 21:57:26.751779 INFO::Total function execution time is 2.30277061462402 s and adjustment time is 2.26057887077332 s ( 98.17 )
2024-10-16 21:57:26.882272 INFO::Formatting Data.
2024-10-16 21:57:26.882972 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:26.883811 INFO::Removing potential empty rows and columns
2024-10-16 21:57:26.884846 INFO::Found 0 missing values.
2024-10-16 21:57:26.888259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:26.888807 INFO::Done
2024-10-16 21:57:26.889303 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 21:57:26.891873 INFO::Starting hierarchical adjustment
2024-10-16 21:57:26.892538 INFO::Found 3 batches.
2024-10-16 21:57:26.893039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 21:57:26.893614 INFO::Using default BPPARAM
2024-10-16 21:57:26.894118 INFO::Processing subtree level 1
2024-10-16 21:57:26.990412 INFO::Adjusting the last 1 batches sequentially
2024-10-16 21:57:26.99227 INFO::Done
2024-10-16 21:57:26.992929 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 21:57:26.996237 INFO::ASW Batch was 0.235040438853455 prior to batch effect correction and is now -0.124166580829818 .
2024-10-16 21:57:26.996864 INFO::ASW Label was -0.208315509180979 prior to batch effect correction and is now -0.101201319953428 .
2024-10-16 21:57:26.997808 INFO::Total function execution time is 0.115540504455566 s and adjustment time is 0.0998437404632568 s ( 86.41 )
2024-10-16 21:57:27.103286 INFO::Formatting Data.
2024-10-16 21:57:27.104051 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:27.104892 INFO::Removing potential empty rows and columns
2024-10-16 21:57:27.105862 INFO::Found 2 missing values.
2024-10-16 21:57:27.108506 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:27.10901 INFO::Done
2024-10-16 21:57:27.132588 INFO::Found NA in Reference column
2024-10-16 21:57:27.141137 INFO::Require at least two references per batch.
2024-10-16 21:57:27.159724 INFO::Formatting Data.
2024-10-16 21:57:27.16041 INFO::Recognized SummarizedExperiment
2024-10-16 21:57:27.160912 INFO::Typecasting input to dataframe.
2024-10-16 21:57:27.169708 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:27.170756 INFO::Removing potential empty rows and columns
2024-10-16 21:57:27.174067 INFO::Found 0 missing values.
2024-10-16 21:57:27.180254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:27.180828 INFO::Done
2024-10-16 21:57:27.194528 INFO::Formatting Data.
2024-10-16 21:57:27.19513 INFO::Recognized SummarizedExperiment
2024-10-16 21:57:27.195646 INFO::Typecasting input to dataframe.
2024-10-16 21:57:27.21143 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:27.212473 INFO::Removing potential empty rows and columns
2024-10-16 21:57:27.215726 INFO::Found 0 missing values.
2024-10-16 21:57:27.225942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:27.226517 INFO::Done
2024-10-16 21:57:27.240414 INFO::Formatting Data.
2024-10-16 21:57:27.241011 INFO::Recognized SummarizedExperiment
2024-10-16 21:57:27.241504 INFO::Typecasting input to dataframe.
2024-10-16 21:57:27.256781 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:27.257694 INFO::Removing potential empty rows and columns
2024-10-16 21:57:27.258792 INFO::Found 0 missing values.
2024-10-16 21:57:27.259734 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.
2024-10-16 21:57:27.26422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:27.264735 INFO::Done
2024-10-16 21:57:27.274225 INFO::Formatting Data.
2024-10-16 21:57:27.274867 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:27.275677 INFO::Removing potential empty rows and columns
2024-10-16 21:57:27.276677 INFO::Found 0 missing values.
2024-10-16 21:57:27.279547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:27.280117 INFO::Done
2024-10-16 21:57:27.290085 INFO::Formatting Data.
2024-10-16 21:57:27.290733 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:27.291573 INFO::Removing potential empty rows and columns
2024-10-16 21:57:27.292492 INFO::Found 0 missing values.
2024-10-16 21:57:27.295225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:27.295769 INFO::Done
2024-10-16 21:57:27.321676 INFO::Formatting Data.
2024-10-16 21:57:27.322503 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:27.323567 INFO::Removing potential empty rows and columns
2024-10-16 21:57:27.32471 INFO::Found 1 missing values.
2024-10-16 21:57:27.327216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:27.327731 INFO::Done
2024-10-16 21:57:27.344591 INFO::Formatting Data.
2024-10-16 21:57:27.345326 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:27.346154 INFO::Removing potential empty rows and columns
2024-10-16 21:57:27.34717 INFO::Found 2 missing values.
2024-10-16 21:57:27.348033 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.
2024-10-16 21:57:27.350164 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:27.350715 INFO::Done
2024-10-16 21:57:27.359562 INFO::Formatting Data.
2024-10-16 21:57:27.360264 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:27.361107 INFO::Removing potential empty rows and columns
2024-10-16 21:57:27.361986 INFO::Found 2 missing values.
2024-10-16 21:57:27.363469 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:27.363975 INFO::Done
2024-10-16 21:57:27.37341 INFO::Formatting Data.
2024-10-16 21:57:27.374113 INFO::Typecasting input to dataframe.
2024-10-16 21:57:27.374928 INFO::Replacing NaNs with NAs.
2024-10-16 21:57:27.375736 INFO::Removing potential empty rows and columns
2024-10-16 21:57:27.376686 INFO::Found 0 missing values.
2024-10-16 21:57:27.37946 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 21:57:27.379963 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.536 3.440 19.538
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.876 | 1.579 | 18.310 | |
| compute_asw | 0.021 | 0.004 | 0.025 | |
| count_existing | 0.013 | 0.003 | 0.016 | |
| generate_data_covariables | 0.013 | 0.001 | 0.014 | |
| generate_dataset | 0.013 | 0.000 | 0.013 | |