Yannis Schumann
| Snapshot Date: 2024-07-21 14:00 -0400 (Sun, 21 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 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" | 4747 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
| 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: 2024-07-21 22:00:25 -0400 (Sun, 21 Jul 2024) |
| EndedAt: 2024-07-21 22:01:53 -0400 (Sun, 21 Jul 2024) |
| EllapsedTime: 87.2 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 22.04.4 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 24.673 1.33 17.945
* 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")
2024-07-21 22:01:17.318726 INFO::Formatting Data.
2024-07-21 22:01:17.320226 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:17.330746 INFO::Removing potential empty rows and columns
2024-07-21 22:01:17.57931 INFO::Found 0 missing values.
2024-07-21 22:01:17.58251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:17.583132 INFO::Done
2024-07-21 22:01:17.583645 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:17.595229 INFO::Starting hierarchical adjustment
2024-07-21 22:01:17.596057 INFO::Found 3 batches.
2024-07-21 22:01:17.596585 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:17.597673 INFO::Using default BPPARAM
2024-07-21 22:01:17.59819 INFO::Processing subtree level 1
2024-07-21 22:01:17.68462 INFO::Adjusting the last 1 batches sequentially
2024-07-21 22:01:17.686295 INFO::Done
2024-07-21 22:01:17.686908 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:17.689368 INFO::ASW Batch was -0.0295698959483754 prior to batch effect correction and is now -0.0295698959483754 .
2024-07-21 22:01:17.690439 INFO::Total function execution time is 0.37252402305603 s and adjustment time is 0.090404748916626 s ( 24.27 )
2024-07-21 22:01:17.703986 INFO::Formatting Data.
2024-07-21 22:01:17.704722 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:17.705607 INFO::Removing potential empty rows and columns
2024-07-21 22:01:17.706674 INFO::Found 0 missing values.
2024-07-21 22:01:17.707607 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-21 22:01:17.718413 INFO::Formatting Data.
2024-07-21 22:01:17.719168 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:17.720075 INFO::Removing potential empty rows and columns
2024-07-21 22:01:17.72113 INFO::Found 0 missing values.
2024-07-21 22:01:17.722068 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-21 22:01:17.737772 INFO::Formatting Data.
2024-07-21 22:01:17.738545 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:17.73938 INFO::Removing potential empty rows and columns
2024-07-21 22:01:17.740372 INFO::Found 0 missing values.
2024-07-21 22:01:17.741247 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-21 22:01:17.745447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:17.74596 INFO::Done
2024-07-21 22:01:17.746452 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:17.748392 INFO::Starting hierarchical adjustment
2024-07-21 22:01:17.749054 INFO::Found 2 batches.
2024-07-21 22:01:17.749554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:17.750176 INFO::Using default BPPARAM
2024-07-21 22:01:17.750675 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:17.751554 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:17.772433 INFO::Done
2024-07-21 22:01:17.773114 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:17.775032 INFO::ASW Batch was -0.015049001427617 prior to batch effect correction and is now -0.0571464576850038 .
2024-07-21 22:01:17.775787 INFO::Total function execution time is 0.0381002426147461 s and adjustment time is 0.0234956741333008 s ( 61.67 )
2024-07-21 22:01:17.778355 INFO::Formatting Data.
2024-07-21 22:01:17.77894 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:17.78881 INFO::Formatting Data.
2024-07-21 22:01:17.789571 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:17.790463 INFO::Removing potential empty rows and columns
2024-07-21 22:01:17.791435 INFO::Found 0 missing values.
2024-07-21 22:01:17.794152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:17.794658 INFO::Done
2024-07-21 22:01:17.795137 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:17.79702 INFO::Starting hierarchical adjustment
2024-07-21 22:01:17.797673 INFO::Found 2 batches.
2024-07-21 22:01:17.798167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:17.798767 INFO::Using default BPPARAM
2024-07-21 22:01:17.79925 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:17.800131 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:17.814092 INFO::Done
2024-07-21 22:01:17.814722 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:17.816625 INFO::ASW Batch was 0.0692670514175189 prior to batch effect correction and is now -0.0915025693534546 .
2024-07-21 22:01:17.817379 INFO::Total function execution time is 0.0286519527435303 s and adjustment time is 0.0165517330169678 s ( 57.77 )
2024-07-21 22:01:17.818416 INFO::Formatting Data.
2024-07-21 22:01:17.819003 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:17.819814 INFO::Removing potential empty rows and columns
2024-07-21 22:01:17.820792 INFO::Found 0 missing values.
2024-07-21 22:01:17.823475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:17.823983 INFO::Done
2024-07-21 22:01:17.824481 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:17.826337 INFO::Starting hierarchical adjustment
2024-07-21 22:01:17.826998 INFO::Found 2 batches.
2024-07-21 22:01:17.827491 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:17.828068 INFO::Using default BPPARAM
2024-07-21 22:01:17.828556 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:17.829391 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:17.843479 INFO::Done
2024-07-21 22:01:17.844113 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:17.846026 INFO::ASW Batch was 0.0692670514175189 prior to batch effect correction and is now -0.0915025693534546 .
2024-07-21 22:01:17.846775 INFO::Total function execution time is 0.0283517837524414 s and adjustment time is 0.0166101455688477 s ( 58.59 )
2024-07-21 22:01:20.013552 INFO::Formatting Data.
2024-07-21 22:01:20.014373 INFO::Recognized SummarizedExperiment
2024-07-21 22:01:20.014886 INFO::Typecasting input to dataframe.
2024-07-21 22:01:20.048675 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:20.05004 INFO::Removing potential empty rows and columns
2024-07-21 22:01:20.054108 INFO::Found 0 missing values.
2024-07-21 22:01:20.060242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:20.060989 INFO::Done
2024-07-21 22:01:20.061489 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:20.065099 INFO::Starting hierarchical adjustment
2024-07-21 22:01:20.06575 INFO::Found 2 batches.
2024-07-21 22:01:20.066208 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:20.06724 INFO::Using default BPPARAM
2024-07-21 22:01:20.067717 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:20.068673 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:20.149976 INFO::Done
2024-07-21 22:01:20.150635 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:20.153515 INFO::ASW Batch was 3.81446038808709e-05 prior to batch effect correction and is now -0.0909255617993466 .
2024-07-21 22:01:20.154235 INFO::Total function execution time is 0.141093730926514 s and adjustment time is 0.084341287612915 s ( 59.78 )
2024-07-21 22:01:20.168978 INFO::Formatting Data.
2024-07-21 22:01:20.169607 INFO::Recognized SummarizedExperiment
2024-07-21 22:01:20.170049 INFO::Typecasting input to dataframe.
2024-07-21 22:01:20.17758 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:20.178566 INFO::Removing potential empty rows and columns
2024-07-21 22:01:20.181445 INFO::Found 0 missing values.
2024-07-21 22:01:20.18681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:20.187276 INFO::Done
2024-07-21 22:01:20.187722 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:20.190552 INFO::Starting hierarchical adjustment
2024-07-21 22:01:20.191175 INFO::Found 2 batches.
2024-07-21 22:01:20.191618 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:20.19213 INFO::Using default BPPARAM
2024-07-21 22:01:20.192564 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:20.193396 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:20.212932 INFO::Done
2024-07-21 22:01:20.213607 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:20.216645 INFO::ASW Batch was -0.00205862239550938 prior to batch effect correction and is now -0.00205862239550938 .
2024-07-21 22:01:20.217369 INFO::Total function execution time is 0.0483698844909668 s and adjustment time is 0.0218307971954346 s ( 45.13 )
2024-07-21 22:01:20.232428 INFO::Formatting Data.
2024-07-21 22:01:20.233139 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:20.233931 INFO::Removing potential empty rows and columns
2024-07-21 22:01:20.234771 INFO::Found 0 missing values.
2024-07-21 22:01:20.237126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:20.237573 INFO::Done
2024-07-21 22:01:20.238004 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:20.239704 INFO::Starting hierarchical adjustment
2024-07-21 22:01:20.240302 INFO::Found 3 batches.
2024-07-21 22:01:20.240732 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:20.241243 INFO::Using default BPPARAM
2024-07-21 22:01:20.241678 INFO::Processing subtree level 1
2024-07-21 22:01:20.386354 INFO::Adjusting the last 1 batches sequentially
2024-07-21 22:01:20.388111 INFO::Done
2024-07-21 22:01:20.388749 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:20.39114 INFO::ASW Batch was -0.0890739971216207 prior to batch effect correction and is now -0.181596096449258 .
2024-07-21 22:01:20.392059 INFO::Total function execution time is 0.159626483917236 s and adjustment time is 0.147896766662598 s ( 92.65 )
2024-07-21 22:01:20.407701 INFO::Skipping initial DF formatting
2024-07-21 22:01:20.408539 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:20.413133 INFO::Starting hierarchical adjustment
2024-07-21 22:01:20.413909 INFO::Found 5 batches.
2024-07-21 22:01:20.414441 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:20.415103 INFO::Using default BPPARAM
2024-07-21 22:01:20.415657 INFO::Processing subtree level 1
2024-07-21 22:01:20.54939 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:20.551256 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:20.572781 INFO::Done
2024-07-21 22:01:20.573601 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:20.57817 INFO::ASW Batch was 0.500189445844671 prior to batch effect correction and is now 0.500189445844671 .
2024-07-21 22:01:20.578869 INFO::ASW Label was 0.369923613008409 prior to batch effect correction and is now 0.369923613008409 .
2024-07-21 22:01:20.579754 INFO::Total function execution time is 0.172161340713501 s and adjustment time is 0.158937931060791 s ( 92.32 )
2024-07-21 22:01:20.597896 INFO::Formatting Data.
2024-07-21 22:01:20.598764 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:20.599708 INFO::Removing potential empty rows and columns
2024-07-21 22:01:20.600738 INFO::Found 0 missing values.
2024-07-21 22:01:20.604743 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:20.605278 INFO::Done
2024-07-21 22:01:20.605803 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:20.60902 INFO::Starting hierarchical adjustment
2024-07-21 22:01:20.609743 INFO::Found 5 batches.
2024-07-21 22:01:20.610272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:20.610915 INFO::Using default BPPARAM
2024-07-21 22:01:20.611444 INFO::Processing subtree level 1
2024-07-21 22:01:20.736523 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:20.738254 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:20.75483 INFO::Done
2024-07-21 22:01:20.75563 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:20.759093 INFO::ASW Batch was 0.555362895734184 prior to batch effect correction and is now 0.00807032725514847 .
2024-07-21 22:01:20.759786 INFO::ASW Label was 0.249304513537182 prior to batch effect correction and is now 0.715311896851439 .
2024-07-21 22:01:20.760696 INFO::Total function execution time is 0.162920951843262 s and adjustment time is 0.145195722579956 s ( 89.12 )
2024-07-21 22:01:20.76162 INFO::Formatting Data.
2024-07-21 22:01:20.76226 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:20.763153 INFO::Removing potential empty rows and columns
2024-07-21 22:01:20.76415 INFO::Found 0 missing values.
2024-07-21 22:01:20.768179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:20.768712 INFO::Done
2024-07-21 22:01:20.769218 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:20.772278 INFO::Starting hierarchical adjustment
2024-07-21 22:01:20.772975 INFO::Found 5 batches.
2024-07-21 22:01:20.773489 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:20.774124 INFO::Using default BPPARAM
2024-07-21 22:01:20.774642 INFO::Processing subtree level 1
2024-07-21 22:01:20.896332 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:20.897931 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:20.912563 INFO::Done
2024-07-21 22:01:20.913267 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:20.916439 INFO::ASW Batch was 0.555362895734184 prior to batch effect correction and is now 0.00807032725514847 .
2024-07-21 22:01:20.917037 INFO::ASW Label was 0.249304513537182 prior to batch effect correction and is now 0.715311896851439 .
2024-07-21 22:01:20.917819 INFO::Total function execution time is 0.156235456466675 s and adjustment time is 0.139708518981934 s ( 89.42 )
2024-07-21 22:01:20.930351 INFO::Formatting Data.
2024-07-21 22:01:20.931112 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:20.931987 INFO::Removing potential empty rows and columns
2024-07-21 22:01:20.932909 INFO::Found 0 missing values.
2024-07-21 22:01:20.936783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:20.937285 INFO::Done
2024-07-21 22:01:20.937776 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:20.940636 INFO::Starting hierarchical adjustment
2024-07-21 22:01:20.941314 INFO::Found 5 batches.
2024-07-21 22:01:20.941817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:20.942447 INFO::Using default BPPARAM
2024-07-21 22:01:20.942965 INFO::Processing subtree level 1
2024-07-21 22:01:21.052946 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:21.054618 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:21.070253 INFO::Done
2024-07-21 22:01:21.071039 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:21.074406 INFO::ASW Batch was 0.408546689849904 prior to batch effect correction and is now 0.0392380489100185 .
2024-07-21 22:01:21.075054 INFO::ASW Label was 0.407137652716712 prior to batch effect correction and is now 0.710277003299214 .
2024-07-21 22:01:21.075917 INFO::Total function execution time is 0.145584106445312 s and adjustment time is 0.129028797149658 s ( 88.63 )
2024-07-21 22:01:21.076799 INFO::Formatting Data.
2024-07-21 22:01:21.077411 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:21.078266 INFO::Removing potential empty rows and columns
2024-07-21 22:01:21.07922 INFO::Found 0 missing values.
2024-07-21 22:01:21.087797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:21.088783 INFO::Done
2024-07-21 22:01:21.089427 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:21.093383 INFO::Starting hierarchical adjustment
2024-07-21 22:01:21.094177 INFO::Found 5 batches.
2024-07-21 22:01:21.094804 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:21.095479 INFO::Using default BPPARAM
2024-07-21 22:01:21.096061 INFO::Processing subtree level 1
2024-07-21 22:01:21.215167 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:21.21697 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:21.233464 INFO::Done
2024-07-21 22:01:21.234174 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:21.237396 INFO::ASW Batch was 0.408546689849904 prior to batch effect correction and is now 0.0392380489100185 .
2024-07-21 22:01:21.238078 INFO::ASW Label was 0.407137652716712 prior to batch effect correction and is now 0.710277003299214 .
2024-07-21 22:01:21.238976 INFO::Total function execution time is 0.162191867828369 s and adjustment time is 0.139432191848755 s ( 85.97 )
2024-07-21 22:01:21.252457 INFO::Formatting Data.
2024-07-21 22:01:21.253241 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:21.254202 INFO::Removing potential empty rows and columns
2024-07-21 22:01:21.255245 INFO::Found 0 missing values.
2024-07-21 22:01:21.257954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:21.258489 INFO::Done
2024-07-21 22:01:21.258997 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:21.261969 INFO::Starting hierarchical adjustment
2024-07-21 22:01:21.262699 INFO::Found 2 batches.
2024-07-21 22:01:21.263252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:21.2639 INFO::Using default BPPARAM
2024-07-21 22:01:21.26444 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:21.26537 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:21.28003 INFO::Done
2024-07-21 22:01:21.280711 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:21.283589 INFO::ASW Batch was 0.441530726149814 prior to batch effect correction and is now -0.00948704353780031 .
2024-07-21 22:01:21.284161 INFO::ASW Label was 0.602152753750003 prior to batch effect correction and is now 0.891380598078576 .
2024-07-21 22:01:21.284967 INFO::Total function execution time is 0.0326099395751953 s and adjustment time is 0.0174651145935059 s ( 53.56 )
2024-07-21 22:01:21.285756 INFO::Formatting Data.
2024-07-21 22:01:21.286363 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:21.28721 INFO::Removing potential empty rows and columns
2024-07-21 22:01:21.288187 INFO::Found 0 missing values.
2024-07-21 22:01:21.290851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:21.291401 INFO::Done
2024-07-21 22:01:21.291934 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:21.294961 INFO::Starting hierarchical adjustment
2024-07-21 22:01:21.295667 INFO::Found 2 batches.
2024-07-21 22:01:21.296249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:21.296894 INFO::Using default BPPARAM
2024-07-21 22:01:21.297426 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:21.298386 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:21.313743 INFO::Done
2024-07-21 22:01:21.314384 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:21.317271 INFO::ASW Batch was 0.441530726149814 prior to batch effect correction and is now -0.00948704353780031 .
2024-07-21 22:01:21.317826 INFO::ASW Label was 0.602152753750003 prior to batch effect correction and is now 0.891380598078576 .
2024-07-21 22:01:21.318588 INFO::Total function execution time is 0.0328495502471924 s and adjustment time is 0.0182247161865234 s ( 55.48 )
2024-07-21 22:01:21.329252 INFO::Formatting Data.
2024-07-21 22:01:21.329948 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:21.330832 INFO::Removing potential empty rows and columns
2024-07-21 22:01:21.331704 INFO::Found 0 missing values.
2024-07-21 22:01:21.33376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:21.334308 INFO::Done
2024-07-21 22:01:21.334826 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:21.336662 INFO::Starting hierarchical adjustment
2024-07-21 22:01:21.337369 INFO::Found 2 batches.
2024-07-21 22:01:21.337951 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:21.338523 INFO::Using default BPPARAM
2024-07-21 22:01:21.339024 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:21.339897 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:21.387223 INFO::Done
2024-07-21 22:01:21.3879 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:21.389677 INFO::ASW Batch was -0.142937247113216 prior to batch effect correction and is now -0.149692035698836 .
2024-07-21 22:01:21.390404 INFO::Total function execution time is 0.0612213611602783 s and adjustment time is 0.0500178337097168 s ( 81.7 )
2024-07-21 22:01:21.401466 INFO::Formatting Data.
2024-07-21 22:01:21.402212 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:21.403066 INFO::Removing potential empty rows and columns
2024-07-21 22:01:21.404044 INFO::Found 0 missing values.
2024-07-21 22:01:21.405224 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-21 22:01:21.409736 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:21.410278 INFO::Done
2024-07-21 22:01:21.410769 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:21.41363 INFO::Starting hierarchical adjustment
2024-07-21 22:01:21.414284 INFO::Found 2 batches.
2024-07-21 22:01:21.414776 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:21.41535 INFO::Using default BPPARAM
2024-07-21 22:01:21.415854 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:21.416809 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:21.433064 INFO::Done
2024-07-21 22:01:21.433722 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:21.436634 INFO::ASW Batch was 0.795395946233829 prior to batch effect correction and is now 0.20378511798939 .
2024-07-21 22:01:21.437181 INFO::ASW Label was 0.346647959182125 prior to batch effect correction and is now 0.815628207958747 .
2024-07-21 22:01:21.437892 INFO::Total function execution time is 0.0364944934844971 s and adjustment time is 0.0188987255096436 s ( 51.79 )
2024-07-21 22:01:21.438682 INFO::Formatting Data.
2024-07-21 22:01:21.439269 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:21.440152 INFO::Removing potential empty rows and columns
2024-07-21 22:01:21.441108 INFO::Found 0 missing values.
2024-07-21 22:01:21.441992 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-21 22:01:21.446318 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:21.446827 INFO::Done
2024-07-21 22:01:21.447365 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:21.450257 INFO::Starting hierarchical adjustment
2024-07-21 22:01:21.450932 INFO::Found 2 batches.
2024-07-21 22:01:21.451453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:21.452083 INFO::Using default BPPARAM
2024-07-21 22:01:21.452589 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:21.453537 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:21.469968 INFO::Done
2024-07-21 22:01:21.470662 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:21.473607 INFO::ASW Batch was 0.795395946233829 prior to batch effect correction and is now 0.20378511798939 .
2024-07-21 22:01:21.474181 INFO::ASW Label was 0.346647959182125 prior to batch effect correction and is now 0.815628207958747 .
2024-07-21 22:01:21.474939 INFO::Total function execution time is 0.0362594127655029 s and adjustment time is 0.0191466808319092 s ( 52.8 )
2024-07-21 22:01:21.681891 INFO::Formatting Data.
2024-07-21 22:01:21.682894 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:21.683926 INFO::Removing potential empty rows and columns
2024-07-21 22:01:21.685046 INFO::Found 0 missing values.
2024-07-21 22:01:21.688147 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:21.688675 INFO::Done
2024-07-21 22:01:21.689181 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:21.691381 INFO::Starting hierarchical adjustment
2024-07-21 22:01:21.692114 INFO::Found 3 batches.
2024-07-21 22:01:21.692631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:21.693255 INFO::Using default BPPARAM
2024-07-21 22:01:21.693778 INFO::Processing subtree level 1
2024-07-21 22:01:21.791319 INFO::Adjusting the last 1 batches sequentially
2024-07-21 22:01:21.793266 INFO::Done
2024-07-21 22:01:21.793952 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:21.796637 INFO::ASW Batch was 0.0120929279688295 prior to batch effect correction and is now 0.0120929279688295 .
2024-07-21 22:01:21.797641 INFO::Total function execution time is 0.116060256958008 s and adjustment time is 0.101309776306152 s ( 87.29 )
2024-07-21 22:01:21.798826 INFO::Formatting Data.
2024-07-21 22:01:21.799501 INFO::Typecasting input to dataframe.
2024-07-21 22:01:21.800308 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:21.801227 INFO::Removing potential empty rows and columns
2024-07-21 22:01:21.802331 INFO::Found 0 missing values.
2024-07-21 22:01:21.805338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:21.805872 INFO::Done
2024-07-21 22:01:21.806428 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:21.808388 INFO::Starting hierarchical adjustment
2024-07-21 22:01:21.809092 INFO::Found 3 batches.
2024-07-21 22:01:21.809621 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:21.810234 INFO::Using default BPPARAM
2024-07-21 22:01:21.810784 INFO::Processing subtree level 1
2024-07-21 22:01:21.897659 INFO::Adjusting the last 1 batches sequentially
2024-07-21 22:01:21.899369 INFO::Done
2024-07-21 22:01:21.900028 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:21.902377 INFO::ASW Batch was 0.0120929279688295 prior to batch effect correction and is now 0.0120929279688295 .
2024-07-21 22:01:21.903301 INFO::Total function execution time is 0.104490280151367 s and adjustment time is 0.0903968811035156 s ( 86.51 )
2024-07-21 22:01:21.91526 INFO::Formatting Data.
2024-07-21 22:01:21.916062 INFO::Typecasting input to dataframe.
2024-07-21 22:01:21.916877 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:21.91771 INFO::Removing potential empty rows and columns
2024-07-21 22:01:21.91873 INFO::Found 0 missing values.
2024-07-21 22:01:21.921578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:21.922088 INFO::Done
2024-07-21 22:01:21.922567 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:21.92452 INFO::Starting hierarchical adjustment
2024-07-21 22:01:21.925254 INFO::Found 3 batches.
2024-07-21 22:01:21.925771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:21.926364 INFO::Using default BPPARAM
2024-07-21 22:01:21.926864 INFO::Processing subtree level 1
2024-07-21 22:01:22.015413 INFO::Adjusting the last 1 batches sequentially
2024-07-21 22:01:22.017116 INFO::Done
2024-07-21 22:01:22.017744 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:22.020226 INFO::ASW Batch was -0.124182287069807 prior to batch effect correction and is now -0.124182287069807 .
2024-07-21 22:01:22.021153 INFO::Total function execution time is 0.105913162231445 s and adjustment time is 0.091989278793335 s ( 86.85 )
2024-07-21 22:01:22.177652 INFO::Formatting Data.
2024-07-21 22:01:22.178915 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:22.180748 INFO::Removing potential empty rows and columns
2024-07-21 22:01:22.185245 INFO::Found 1000 missing values.
2024-07-21 22:01:22.214777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:22.215819 INFO::Done
2024-07-21 22:01:22.216663 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:22.225398 INFO::Starting hierarchical adjustment
2024-07-21 22:01:22.226554 INFO::Found 10 batches.
2024-07-21 22:01:22.227348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:22.228328 INFO::Using default BPPARAM
2024-07-21 22:01:22.229133 INFO::Processing subtree level 1
2024-07-21 22:01:22.548509 INFO::Processing subtree level 2
2024-07-21 22:01:22.769226 INFO::Adjusting the last 1 batches sequentially
2024-07-21 22:01:22.771186 INFO::Done
2024-07-21 22:01:22.771885 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:22.777603 INFO::ASW Batch was 0.458771151171291 prior to batch effect correction and is now 0.458771151171291 .
2024-07-21 22:01:22.778576 INFO::ASW Label was 0.365186660302356 prior to batch effect correction and is now 0.365186660302356 .
2024-07-21 22:01:22.779994 INFO::Total function execution time is 0.602406024932861 s and adjustment time is 0.544893026351929 s ( 90.45 )
2024-07-21 22:01:22.781399 INFO::Formatting Data.
2024-07-21 22:01:22.782418 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:22.784306 INFO::Removing potential empty rows and columns
2024-07-21 22:01:22.788748 INFO::Found 1000 missing values.
2024-07-21 22:01:22.839938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:22.840676 INFO::Done
2024-07-21 22:01:22.84125 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:22.847329 INFO::Starting hierarchical adjustment
2024-07-21 22:01:22.848226 INFO::Found 10 batches.
2024-07-21 22:01:24.102243 INFO::Set up parallel execution backend with 2 workers
2024-07-21 22:01:24.103668 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-21 22:01:25.316234 INFO::Adjusting the last 2 batches sequentially
2024-07-21 22:01:25.317955 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-21 22:01:25.33387 INFO::Done
2024-07-21 22:01:25.334507 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:25.339268 INFO::ASW Batch was 0.458771151171291 prior to batch effect correction and is now 0.458771151171291 .
2024-07-21 22:01:25.33982 INFO::ASW Label was 0.365186660302356 prior to batch effect correction and is now 0.365186660302356 .
2024-07-21 22:01:25.340534 INFO::Total function execution time is 2.55931186676025 s and adjustment time is 2.48580765724182 s ( 97.13 )
2024-07-21 22:01:25.470134 INFO::Formatting Data.
2024-07-21 22:01:25.470915 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.471832 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.472829 INFO::Found 0 missing values.
2024-07-21 22:01:25.476189 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.476718 INFO::Done
2024-07-21 22:01:25.477201 INFO::Acquiring quality metrics before batch effect correction.
2024-07-21 22:01:25.479742 INFO::Starting hierarchical adjustment
2024-07-21 22:01:25.480415 INFO::Found 3 batches.
2024-07-21 22:01:25.480899 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-21 22:01:25.481442 INFO::Using default BPPARAM
2024-07-21 22:01:25.481912 INFO::Processing subtree level 1
2024-07-21 22:01:25.576502 INFO::Adjusting the last 1 batches sequentially
2024-07-21 22:01:25.578123 INFO::Done
2024-07-21 22:01:25.578729 INFO::Acquiring quality metrics after batch effect correction.
2024-07-21 22:01:25.581711 INFO::ASW Batch was 0.262639159223889 prior to batch effect correction and is now -0.179193158302819 .
2024-07-21 22:01:25.582295 INFO::ASW Label was -0.159794583244445 prior to batch effect correction and is now 0.0597591596621068 .
2024-07-21 22:01:25.583141 INFO::Total function execution time is 0.113049268722534 s and adjustment time is 0.0978224277496338 s ( 86.53 )
2024-07-21 22:01:25.688836 INFO::Formatting Data.
2024-07-21 22:01:25.689602 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.69045 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.691396 INFO::Found 2 missing values.
2024-07-21 22:01:25.693969 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.694464 INFO::Done
2024-07-21 22:01:25.718401 INFO::Found NA in Reference column
2024-07-21 22:01:25.726959 INFO::Require at least two references per batch.
2024-07-21 22:01:25.745549 INFO::Formatting Data.
2024-07-21 22:01:25.746325 INFO::Recognized SummarizedExperiment
2024-07-21 22:01:25.746842 INFO::Typecasting input to dataframe.
2024-07-21 22:01:25.755771 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.756891 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.760147 INFO::Found 0 missing values.
2024-07-21 22:01:25.766269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.766897 INFO::Done
2024-07-21 22:01:25.781344 INFO::Formatting Data.
2024-07-21 22:01:25.782058 INFO::Recognized SummarizedExperiment
2024-07-21 22:01:25.782579 INFO::Typecasting input to dataframe.
2024-07-21 22:01:25.799434 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.800619 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.804093 INFO::Found 0 missing values.
2024-07-21 22:01:25.814653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.81533 INFO::Done
2024-07-21 22:01:25.830038 INFO::Formatting Data.
2024-07-21 22:01:25.830759 INFO::Recognized SummarizedExperiment
2024-07-21 22:01:25.831278 INFO::Typecasting input to dataframe.
2024-07-21 22:01:25.847447 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.848449 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.849458 INFO::Found 0 missing values.
2024-07-21 22:01:25.850514 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-21 22:01:25.854971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.855488 INFO::Done
2024-07-21 22:01:25.865122 INFO::Formatting Data.
2024-07-21 22:01:25.865874 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.866714 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.867868 INFO::Found 0 missing values.
2024-07-21 22:01:25.870854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.871358 INFO::Done
2024-07-21 22:01:25.881799 INFO::Formatting Data.
2024-07-21 22:01:25.882533 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.883377 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.884373 INFO::Found 0 missing values.
2024-07-21 22:01:25.887134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.887678 INFO::Done
2024-07-21 22:01:25.921145 INFO::Formatting Data.
2024-07-21 22:01:25.921998 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.923022 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.9243 INFO::Found 1 missing values.
2024-07-21 22:01:25.926848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.927367 INFO::Done
2024-07-21 22:01:25.945915 INFO::Formatting Data.
2024-07-21 22:01:25.946764 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.947627 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.948658 INFO::Found 2 missing values.
2024-07-21 22:01:25.949587 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-21 22:01:25.951895 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.952447 INFO::Done
2024-07-21 22:01:25.962457 INFO::Formatting Data.
2024-07-21 22:01:25.963221 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.964102 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.96504 INFO::Found 2 missing values.
2024-07-21 22:01:25.96664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.967165 INFO::Done
2024-07-21 22:01:25.977639 INFO::Formatting Data.
2024-07-21 22:01:25.978435 INFO::Typecasting input to dataframe.
2024-07-21 22:01:25.979277 INFO::Replacing NaNs with NAs.
2024-07-21 22:01:25.980207 INFO::Removing potential empty rows and columns
2024-07-21 22:01:25.981262 INFO::Found 0 missing values.
2024-07-21 22:01:25.98434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-21 22:01:25.984887 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.588 3.627 19.774
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.673 | 1.330 | 17.945 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.000 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.007 | 0.004 | 0.012 | |