Yannis Schumann
| Snapshot Date: 2024-08-14 14:00 -0400 (Wed, 14 Aug 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-15 11:39 -0400 (Thu, 15 Aug 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 157/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.2 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.2.tar.gz |
| StartedAt: 2024-08-14 21:16:48 -0400 (Wed, 14 Aug 2024) |
| EndedAt: 2024-08-14 21:18:19 -0400 (Wed, 14 Aug 2024) |
| EllapsedTime: 91.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-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 ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 26.395 1.457 19.365
* 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-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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")
2024-08-14 21:17:43.240363 INFO::Formatting Data.
2024-08-14 21:17:43.241901 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:43.253148 INFO::Removing potential empty rows and columns
2024-08-14 21:17:43.512142 INFO::Found 0 missing values.
2024-08-14 21:17:43.515477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:43.516154 INFO::Done
2024-08-14 21:17:43.516677 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:43.528779 INFO::Starting hierarchical adjustment
2024-08-14 21:17:43.529596 INFO::Found 3 batches.
2024-08-14 21:17:43.530115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:43.53122 INFO::Using default BPPARAM
2024-08-14 21:17:43.531736 INFO::Processing subtree level 1
2024-08-14 21:17:43.625822 INFO::Adjusting the last 1 batches sequentially
2024-08-14 21:17:43.628057 INFO::Done
2024-08-14 21:17:43.628895 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:43.632102 INFO::ASW Batch was -0.0195234125645255 prior to batch effect correction and is now -0.0195234125645255 .
2024-08-14 21:17:43.633386 INFO::Total function execution time is 0.393873453140259 s and adjustment time is 0.0985665321350098 s ( 25.02 )
2024-08-14 21:17:43.64995 INFO::Formatting Data.
2024-08-14 21:17:43.650908 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:43.652133 INFO::Removing potential empty rows and columns
2024-08-14 21:17:43.653452 INFO::Found 0 missing values.
2024-08-14 21:17:43.654596 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.
2024-08-14 21:17:43.668144 INFO::Formatting Data.
2024-08-14 21:17:43.669053 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:43.670188 INFO::Removing potential empty rows and columns
2024-08-14 21:17:43.67143 INFO::Found 0 missing values.
2024-08-14 21:17:43.672673 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.
2024-08-14 21:17:43.690691 INFO::Formatting Data.
2024-08-14 21:17:43.691399 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:43.692237 INFO::Removing potential empty rows and columns
2024-08-14 21:17:43.693233 INFO::Found 0 missing values.
2024-08-14 21:17:43.69408 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.
2024-08-14 21:17:43.698464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:43.698989 INFO::Done
2024-08-14 21:17:43.699462 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:43.70146 INFO::Starting hierarchical adjustment
2024-08-14 21:17:43.702111 INFO::Found 2 batches.
2024-08-14 21:17:43.702598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:43.70317 INFO::Using default BPPARAM
2024-08-14 21:17:43.703651 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:43.704507 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:43.73413 INFO::Done
2024-08-14 21:17:43.734957 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:43.737202 INFO::ASW Batch was 0.0104148082545606 prior to batch effect correction and is now -0.114132230112192 .
2024-08-14 21:17:43.737988 INFO::Total function execution time is 0.0473587512969971 s and adjustment time is 0.0319952964782715 s ( 67.56 )
2024-08-14 21:17:43.741504 INFO::Formatting Data.
2024-08-14 21:17:43.742094 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:43.750807 INFO::Formatting Data.
2024-08-14 21:17:43.751391 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:43.752192 INFO::Removing potential empty rows and columns
2024-08-14 21:17:43.753195 INFO::Found 0 missing values.
2024-08-14 21:17:43.755878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:43.756371 INFO::Done
2024-08-14 21:17:43.756828 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:43.758732 INFO::Starting hierarchical adjustment
2024-08-14 21:17:43.759387 INFO::Found 2 batches.
2024-08-14 21:17:43.759856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:43.760452 INFO::Using default BPPARAM
2024-08-14 21:17:43.760932 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:43.761809 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:43.776514 INFO::Done
2024-08-14 21:17:43.777131 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:43.779061 INFO::ASW Batch was 0.0281980546284301 prior to batch effect correction and is now -0.130385578757067 .
2024-08-14 21:17:43.779793 INFO::Total function execution time is 0.0290055274963379 s and adjustment time is 0.0172691345214844 s ( 59.54 )
2024-08-14 21:17:43.780792 INFO::Formatting Data.
2024-08-14 21:17:43.781379 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:43.78217 INFO::Removing potential empty rows and columns
2024-08-14 21:17:43.783149 INFO::Found 0 missing values.
2024-08-14 21:17:43.78585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:43.786332 INFO::Done
2024-08-14 21:17:43.786808 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:43.788654 INFO::Starting hierarchical adjustment
2024-08-14 21:17:43.78932 INFO::Found 2 batches.
2024-08-14 21:17:43.789804 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:43.790349 INFO::Using default BPPARAM
2024-08-14 21:17:43.790829 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:43.791653 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:43.805994 INFO::Done
2024-08-14 21:17:43.806577 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:43.808511 INFO::ASW Batch was 0.0281980546284301 prior to batch effect correction and is now -0.130385578757067 .
2024-08-14 21:17:43.809265 INFO::Total function execution time is 0.0284721851348877 s and adjustment time is 0.016793966293335 s ( 58.98 )
2024-08-14 21:17:46.110831 INFO::Formatting Data.
2024-08-14 21:17:46.111632 INFO::Recognized SummarizedExperiment
2024-08-14 21:17:46.112117 INFO::Typecasting input to dataframe.
2024-08-14 21:17:46.142561 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:46.143675 INFO::Removing potential empty rows and columns
2024-08-14 21:17:46.146682 INFO::Found 0 missing values.
2024-08-14 21:17:46.152315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:46.152795 INFO::Done
2024-08-14 21:17:46.153253 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:46.156364 INFO::Starting hierarchical adjustment
2024-08-14 21:17:46.157103 INFO::Found 2 batches.
2024-08-14 21:17:46.157566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:46.158588 INFO::Using default BPPARAM
2024-08-14 21:17:46.159083 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:46.160007 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:46.212781 INFO::Done
2024-08-14 21:17:46.213457 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:46.21676 INFO::ASW Batch was 0.0132308411216791 prior to batch effect correction and is now -0.0920472429172848 .
2024-08-14 21:17:46.217501 INFO::Total function execution time is 0.107048273086548 s and adjustment time is 0.0558264255523682 s ( 52.15 )
2024-08-14 21:17:46.233759 INFO::Formatting Data.
2024-08-14 21:17:46.234396 INFO::Recognized SummarizedExperiment
2024-08-14 21:17:46.234868 INFO::Typecasting input to dataframe.
2024-08-14 21:17:46.243489 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:46.244516 INFO::Removing potential empty rows and columns
2024-08-14 21:17:46.247745 INFO::Found 0 missing values.
2024-08-14 21:17:46.253948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:46.254445 INFO::Done
2024-08-14 21:17:46.254897 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:46.258023 INFO::Starting hierarchical adjustment
2024-08-14 21:17:46.258653 INFO::Found 2 batches.
2024-08-14 21:17:46.259091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:46.259593 INFO::Using default BPPARAM
2024-08-14 21:17:46.260019 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:46.260882 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:46.281418 INFO::Done
2024-08-14 21:17:46.281999 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:46.28492 INFO::ASW Batch was -0.0155334274605709 prior to batch effect correction and is now -0.0155334274605709 .
2024-08-14 21:17:46.285653 INFO::Total function execution time is 0.0518875122070312 s and adjustment time is 0.0228638648986816 s ( 44.06 )
2024-08-14 21:17:46.30092 INFO::Formatting Data.
2024-08-14 21:17:46.301606 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:46.302364 INFO::Removing potential empty rows and columns
2024-08-14 21:17:46.303295 INFO::Found 0 missing values.
2024-08-14 21:17:46.306062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:46.306537 INFO::Done
2024-08-14 21:17:46.307009 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:46.308899 INFO::Starting hierarchical adjustment
2024-08-14 21:17:46.309584 INFO::Found 3 batches.
2024-08-14 21:17:46.310114 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:46.310638 INFO::Using default BPPARAM
2024-08-14 21:17:46.311112 INFO::Processing subtree level 1
2024-08-14 21:17:46.483171 INFO::Adjusting the last 1 batches sequentially
2024-08-14 21:17:46.485657 INFO::Done
2024-08-14 21:17:46.486317 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:46.488878 INFO::ASW Batch was -0.0268790160118762 prior to batch effect correction and is now -0.156659361724807 .
2024-08-14 21:17:46.48984 INFO::Total function execution time is 0.188916206359863 s and adjustment time is 0.176172733306885 s ( 93.25 )
2024-08-14 21:17:46.504626 INFO::Skipping initial DF formatting
2024-08-14 21:17:46.505324 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:46.509409 INFO::Starting hierarchical adjustment
2024-08-14 21:17:46.510182 INFO::Found 5 batches.
2024-08-14 21:17:46.510706 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:46.511314 INFO::Using default BPPARAM
2024-08-14 21:17:46.511844 INFO::Processing subtree level 1
2024-08-14 21:17:46.639496 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:46.641221 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:46.661418 INFO::Done
2024-08-14 21:17:46.6622 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:46.66648 INFO::ASW Batch was 0.507083805208019 prior to batch effect correction and is now 0.507083805208019 .
2024-08-14 21:17:46.667094 INFO::ASW Label was 0.372710894672815 prior to batch effect correction and is now 0.372710894672815 .
2024-08-14 21:17:46.667943 INFO::Total function execution time is 0.163396596908569 s and adjustment time is 0.151353120803833 s ( 92.63 )
2024-08-14 21:17:46.684735 INFO::Formatting Data.
2024-08-14 21:17:46.685508 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:46.686408 INFO::Removing potential empty rows and columns
2024-08-14 21:17:46.687402 INFO::Found 0 missing values.
2024-08-14 21:17:46.691334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:46.69186 INFO::Done
2024-08-14 21:17:46.69237 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:46.695425 INFO::Starting hierarchical adjustment
2024-08-14 21:17:46.696121 INFO::Found 5 batches.
2024-08-14 21:17:46.696622 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:46.697235 INFO::Using default BPPARAM
2024-08-14 21:17:46.697742 INFO::Processing subtree level 1
2024-08-14 21:17:46.833231 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:46.835088 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:46.852729 INFO::Done
2024-08-14 21:17:46.853549 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:46.857121 INFO::ASW Batch was 0.429486666033161 prior to batch effect correction and is now -0.0772041107308476 .
2024-08-14 21:17:46.85782 INFO::ASW Label was 0.241888938561501 prior to batch effect correction and is now 0.760903005398188 .
2024-08-14 21:17:46.858719 INFO::Total function execution time is 0.17403507232666 s and adjustment time is 0.156698226928711 s ( 90.04 )
2024-08-14 21:17:46.859612 INFO::Formatting Data.
2024-08-14 21:17:46.860252 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:46.861231 INFO::Removing potential empty rows and columns
2024-08-14 21:17:46.86229 INFO::Found 0 missing values.
2024-08-14 21:17:46.866486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:46.867042 INFO::Done
2024-08-14 21:17:46.867559 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:46.870727 INFO::Starting hierarchical adjustment
2024-08-14 21:17:46.871428 INFO::Found 5 batches.
2024-08-14 21:17:46.871943 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:46.872556 INFO::Using default BPPARAM
2024-08-14 21:17:46.873084 INFO::Processing subtree level 1
2024-08-14 21:17:47.00088 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:47.002915 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:47.019719 INFO::Done
2024-08-14 21:17:47.020528 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:47.024233 INFO::ASW Batch was 0.429486666033161 prior to batch effect correction and is now -0.0772041107308476 .
2024-08-14 21:17:47.024881 INFO::ASW Label was 0.241888938561501 prior to batch effect correction and is now 0.760903005398188 .
2024-08-14 21:17:47.025826 INFO::Total function execution time is 0.166173934936523 s and adjustment time is 0.148397207260132 s ( 89.3 )
2024-08-14 21:17:47.04086 INFO::Formatting Data.
2024-08-14 21:17:47.041664 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:47.042665 INFO::Removing potential empty rows and columns
2024-08-14 21:17:47.043766 INFO::Found 0 missing values.
2024-08-14 21:17:47.048137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:47.048694 INFO::Done
2024-08-14 21:17:47.049293 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:47.052566 INFO::Starting hierarchical adjustment
2024-08-14 21:17:47.053352 INFO::Found 5 batches.
2024-08-14 21:17:47.05387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:47.054523 INFO::Using default BPPARAM
2024-08-14 21:17:47.05506 INFO::Processing subtree level 1
2024-08-14 21:17:47.239127 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:47.240695 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:47.256742 INFO::Done
2024-08-14 21:17:47.257456 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:47.260699 INFO::ASW Batch was 0.279730614144144 prior to batch effect correction and is now -0.0925612994151374 .
2024-08-14 21:17:47.261344 INFO::ASW Label was 0.505865283348087 prior to batch effect correction and is now 0.838380076576004 .
2024-08-14 21:17:47.262254 INFO::Total function execution time is 0.221489191055298 s and adjustment time is 0.203529596328735 s ( 91.89 )
2024-08-14 21:17:47.263091 INFO::Formatting Data.
2024-08-14 21:17:47.263715 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:47.264581 INFO::Removing potential empty rows and columns
2024-08-14 21:17:47.265563 INFO::Found 0 missing values.
2024-08-14 21:17:47.269609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:47.270134 INFO::Done
2024-08-14 21:17:47.270636 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:47.273675 INFO::Starting hierarchical adjustment
2024-08-14 21:17:47.274385 INFO::Found 5 batches.
2024-08-14 21:17:47.274892 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:47.275491 INFO::Using default BPPARAM
2024-08-14 21:17:47.276004 INFO::Processing subtree level 1
2024-08-14 21:17:47.446699 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:47.449686 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:47.466967 INFO::Done
2024-08-14 21:17:47.467691 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:47.4712 INFO::ASW Batch was 0.279730614144144 prior to batch effect correction and is now -0.0925612994151374 .
2024-08-14 21:17:47.471871 INFO::ASW Label was 0.505865283348087 prior to batch effect correction and is now 0.838380076576004 .
2024-08-14 21:17:47.472686 INFO::Total function execution time is 0.209588289260864 s and adjustment time is 0.192657232284546 s ( 91.92 )
2024-08-14 21:17:47.48684 INFO::Formatting Data.
2024-08-14 21:17:47.487607 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:47.488558 INFO::Removing potential empty rows and columns
2024-08-14 21:17:47.489668 INFO::Found 0 missing values.
2024-08-14 21:17:47.492442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:47.492952 INFO::Done
2024-08-14 21:17:47.493505 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:47.496541 INFO::Starting hierarchical adjustment
2024-08-14 21:17:47.497344 INFO::Found 2 batches.
2024-08-14 21:17:47.497925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:47.498641 INFO::Using default BPPARAM
2024-08-14 21:17:47.499141 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:47.500038 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:47.515949 INFO::Done
2024-08-14 21:17:47.516611 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:47.519763 INFO::ASW Batch was 0.562785682956931 prior to batch effect correction and is now 0.158785555646686 .
2024-08-14 21:17:47.520339 INFO::ASW Label was 0.594614898449048 prior to batch effect correction and is now 0.781158172817945 .
2024-08-14 21:17:47.521177 INFO::Total function execution time is 0.0343554019927979 s and adjustment time is 0.0187938213348389 s ( 54.7 )
2024-08-14 21:17:47.521958 INFO::Formatting Data.
2024-08-14 21:17:47.522569 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:47.523472 INFO::Removing potential empty rows and columns
2024-08-14 21:17:47.524493 INFO::Found 0 missing values.
2024-08-14 21:17:47.527303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:47.527845 INFO::Done
2024-08-14 21:17:47.528361 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:47.531469 INFO::Starting hierarchical adjustment
2024-08-14 21:17:47.532161 INFO::Found 2 batches.
2024-08-14 21:17:47.532696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:47.533304 INFO::Using default BPPARAM
2024-08-14 21:17:47.533824 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:47.534766 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:47.550592 INFO::Done
2024-08-14 21:17:47.551215 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:47.554213 INFO::ASW Batch was 0.562785682956931 prior to batch effect correction and is now 0.158785555646686 .
2024-08-14 21:17:47.554783 INFO::ASW Label was 0.594614898449048 prior to batch effect correction and is now 0.781158172817945 .
2024-08-14 21:17:47.555507 INFO::Total function execution time is 0.0335586071014404 s and adjustment time is 0.0185718536376953 s ( 55.34 )
2024-08-14 21:17:47.56666 INFO::Formatting Data.
2024-08-14 21:17:47.567364 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:47.568233 INFO::Removing potential empty rows and columns
2024-08-14 21:17:47.569255 INFO::Found 0 missing values.
2024-08-14 21:17:47.571513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:47.572065 INFO::Done
2024-08-14 21:17:47.572556 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:47.574612 INFO::Starting hierarchical adjustment
2024-08-14 21:17:47.575318 INFO::Found 2 batches.
2024-08-14 21:17:47.575831 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:47.576445 INFO::Using default BPPARAM
2024-08-14 21:17:47.576972 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:47.577965 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:47.611649 INFO::Done
2024-08-14 21:17:47.612361 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:47.614461 INFO::ASW Batch was -0.0391666455490707 prior to batch effect correction and is now -0.138505635753215 .
2024-08-14 21:17:47.6153 INFO::Total function execution time is 0.0486993789672852 s and adjustment time is 0.0364608764648438 s ( 74.87 )
2024-08-14 21:17:47.628105 INFO::Formatting Data.
2024-08-14 21:17:47.62894 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:47.630046 INFO::Removing potential empty rows and columns
2024-08-14 21:17:47.631066 INFO::Found 0 missing values.
2024-08-14 21:17:47.63232 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.
2024-08-14 21:17:47.637178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:47.637769 INFO::Done
2024-08-14 21:17:47.638299 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:47.641576 INFO::Starting hierarchical adjustment
2024-08-14 21:17:47.642393 INFO::Found 2 batches.
2024-08-14 21:17:47.642983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:47.643628 INFO::Using default BPPARAM
2024-08-14 21:17:47.644138 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:47.648573 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:47.666981 INFO::Done
2024-08-14 21:17:47.667618 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:47.670906 INFO::ASW Batch was 0.609407119475793 prior to batch effect correction and is now 0.0463967506207699 .
2024-08-14 21:17:47.671503 INFO::ASW Label was 0.458775783870711 prior to batch effect correction and is now 0.844309702832796 .
2024-08-14 21:17:47.672277 INFO::Total function execution time is 0.0442781448364258 s and adjustment time is 0.0247609615325928 s ( 55.92 )
2024-08-14 21:17:47.673158 INFO::Formatting Data.
2024-08-14 21:17:47.673745 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:47.674697 INFO::Removing potential empty rows and columns
2024-08-14 21:17:47.675669 INFO::Found 0 missing values.
2024-08-14 21:17:47.676602 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.
2024-08-14 21:17:47.681624 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:47.682142 INFO::Done
2024-08-14 21:17:47.682631 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:47.685692 INFO::Starting hierarchical adjustment
2024-08-14 21:17:47.686386 INFO::Found 2 batches.
2024-08-14 21:17:47.6869 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:47.687479 INFO::Using default BPPARAM
2024-08-14 21:17:47.687981 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:47.688883 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:47.705724 INFO::Done
2024-08-14 21:17:47.706375 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:47.709437 INFO::ASW Batch was 0.609407119475793 prior to batch effect correction and is now 0.0463967506207699 .
2024-08-14 21:17:47.710031 INFO::ASW Label was 0.458775783870711 prior to batch effect correction and is now 0.844309702832796 .
2024-08-14 21:17:47.710833 INFO::Total function execution time is 0.0377318859100342 s and adjustment time is 0.0194699764251709 s ( 51.6 )
2024-08-14 21:17:47.970269 INFO::Formatting Data.
2024-08-14 21:17:47.971309 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:47.97228 INFO::Removing potential empty rows and columns
2024-08-14 21:17:47.973388 INFO::Found 0 missing values.
2024-08-14 21:17:47.976521 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:47.977131 INFO::Done
2024-08-14 21:17:47.977656 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:47.979868 INFO::Starting hierarchical adjustment
2024-08-14 21:17:47.980577 INFO::Found 3 batches.
2024-08-14 21:17:47.981125 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:47.98174 INFO::Using default BPPARAM
2024-08-14 21:17:47.982263 INFO::Processing subtree level 1
2024-08-14 21:17:48.089213 INFO::Adjusting the last 1 batches sequentially
2024-08-14 21:17:48.091247 INFO::Done
2024-08-14 21:17:48.092035 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:48.095029 INFO::ASW Batch was -0.10832904009905 prior to batch effect correction and is now -0.10832904009905 .
2024-08-14 21:17:48.096131 INFO::Total function execution time is 0.125927209854126 s and adjustment time is 0.110787391662598 s ( 87.98 )
2024-08-14 21:17:48.097278 INFO::Formatting Data.
2024-08-14 21:17:48.097966 INFO::Typecasting input to dataframe.
2024-08-14 21:17:48.098779 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:48.099806 INFO::Removing potential empty rows and columns
2024-08-14 21:17:48.100956 INFO::Found 0 missing values.
2024-08-14 21:17:48.104203 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:48.104779 INFO::Done
2024-08-14 21:17:48.10542 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:48.107661 INFO::Starting hierarchical adjustment
2024-08-14 21:17:48.108431 INFO::Found 3 batches.
2024-08-14 21:17:48.109025 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:48.109663 INFO::Using default BPPARAM
2024-08-14 21:17:48.110217 INFO::Processing subtree level 1
2024-08-14 21:17:48.258895 INFO::Adjusting the last 1 batches sequentially
2024-08-14 21:17:48.260975 INFO::Done
2024-08-14 21:17:48.26178 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:48.264651 INFO::ASW Batch was -0.10832904009905 prior to batch effect correction and is now -0.10832904009905 .
2024-08-14 21:17:48.26576 INFO::Total function execution time is 0.168441534042358 s and adjustment time is 0.152640342712402 s ( 90.62 )
2024-08-14 21:17:48.27983 INFO::Formatting Data.
2024-08-14 21:17:48.280663 INFO::Typecasting input to dataframe.
2024-08-14 21:17:48.281584 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:48.282531 INFO::Removing potential empty rows and columns
2024-08-14 21:17:48.283661 INFO::Found 0 missing values.
2024-08-14 21:17:48.286839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:48.287405 INFO::Done
2024-08-14 21:17:48.287932 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:48.290242 INFO::Starting hierarchical adjustment
2024-08-14 21:17:48.290982 INFO::Found 3 batches.
2024-08-14 21:17:48.291506 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:48.292096 INFO::Using default BPPARAM
2024-08-14 21:17:48.292615 INFO::Processing subtree level 1
2024-08-14 21:17:48.441884 INFO::Adjusting the last 1 batches sequentially
2024-08-14 21:17:48.443811 INFO::Done
2024-08-14 21:17:48.444459 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:48.447029 INFO::ASW Batch was -0.101696151652173 prior to batch effect correction and is now -0.101696151652173 .
2024-08-14 21:17:48.448019 INFO::Total function execution time is 0.16826605796814 s and adjustment time is 0.152993202209473 s ( 90.92 )
2024-08-14 21:17:48.633261 INFO::Formatting Data.
2024-08-14 21:17:48.634039 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:48.635174 INFO::Removing potential empty rows and columns
2024-08-14 21:17:48.638191 INFO::Found 1000 missing values.
2024-08-14 21:17:48.656016 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:48.656693 INFO::Done
2024-08-14 21:17:48.657319 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:48.662772 INFO::Starting hierarchical adjustment
2024-08-14 21:17:48.663481 INFO::Found 10 batches.
2024-08-14 21:17:48.66401 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:48.66459 INFO::Using default BPPARAM
2024-08-14 21:17:48.665139 INFO::Processing subtree level 1
2024-08-14 21:17:48.814495 INFO::Processing subtree level 2
2024-08-14 21:17:48.996187 INFO::Adjusting the last 1 batches sequentially
2024-08-14 21:17:48.998903 INFO::Done
2024-08-14 21:17:48.999873 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:49.008924 INFO::ASW Batch was 0.50241175879244 prior to batch effect correction and is now 0.50241175879244 .
2024-08-14 21:17:49.009995 INFO::ASW Label was 0.356176134742965 prior to batch effect correction and is now 0.356176134742965 .
2024-08-14 21:17:49.011282 INFO::Total function execution time is 0.378031969070435 s and adjustment time is 0.335498571395874 s ( 88.75 )
2024-08-14 21:17:49.012558 INFO::Formatting Data.
2024-08-14 21:17:49.013656 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:49.015445 INFO::Removing potential empty rows and columns
2024-08-14 21:17:49.01997 INFO::Found 1000 missing values.
2024-08-14 21:17:49.051176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:49.052356 INFO::Done
2024-08-14 21:17:49.053347 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:49.062618 INFO::Starting hierarchical adjustment
2024-08-14 21:17:49.063775 INFO::Found 10 batches.
2024-08-14 21:17:50.191585 INFO::Set up parallel execution backend with 2 workers
2024-08-14 21:17:50.193259 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-08-14 21:17:51.292449 INFO::Adjusting the last 2 batches sequentially
2024-08-14 21:17:51.293935 INFO::Adjusting sequential tree level 1 with 2 batches
2024-08-14 21:17:51.30932 INFO::Done
2024-08-14 21:17:51.309937 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:51.314477 INFO::ASW Batch was 0.50241175879244 prior to batch effect correction and is now 0.50241175879244 .
2024-08-14 21:17:51.314994 INFO::ASW Label was 0.356176134742965 prior to batch effect correction and is now 0.356176134742965 .
2024-08-14 21:17:51.315668 INFO::Total function execution time is 2.30325746536255 s and adjustment time is 2.24582433700562 s ( 97.51 )
2024-08-14 21:17:51.446765 INFO::Formatting Data.
2024-08-14 21:17:51.447618 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.448541 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.449654 INFO::Found 0 missing values.
2024-08-14 21:17:51.453308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.453869 INFO::Done
2024-08-14 21:17:51.454349 INFO::Acquiring quality metrics before batch effect correction.
2024-08-14 21:17:51.457139 INFO::Starting hierarchical adjustment
2024-08-14 21:17:51.457825 INFO::Found 3 batches.
2024-08-14 21:17:51.45833 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-08-14 21:17:51.458915 INFO::Using default BPPARAM
2024-08-14 21:17:51.459407 INFO::Processing subtree level 1
2024-08-14 21:17:51.558512 INFO::Adjusting the last 1 batches sequentially
2024-08-14 21:17:51.560189 INFO::Done
2024-08-14 21:17:51.560818 INFO::Acquiring quality metrics after batch effect correction.
2024-08-14 21:17:51.563916 INFO::ASW Batch was 0.212078162503668 prior to batch effect correction and is now -0.114932244433747 .
2024-08-14 21:17:51.564513 INFO::ASW Label was -0.192373364994125 prior to batch effect correction and is now 0.0162670015808709 .
2024-08-14 21:17:51.565438 INFO::Total function execution time is 0.118749380111694 s and adjustment time is 0.102483987808228 s ( 86.3 )
2024-08-14 21:17:51.670626 INFO::Formatting Data.
2024-08-14 21:17:51.671376 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.672179 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.673134 INFO::Found 2 missing values.
2024-08-14 21:17:51.67565 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.676124 INFO::Done
2024-08-14 21:17:51.699406 INFO::Found NA in Reference column
2024-08-14 21:17:51.707512 INFO::Require at least two references per batch.
2024-08-14 21:17:51.725528 INFO::Formatting Data.
2024-08-14 21:17:51.726221 INFO::Recognized SummarizedExperiment
2024-08-14 21:17:51.726706 INFO::Typecasting input to dataframe.
2024-08-14 21:17:51.735374 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.736402 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.739623 INFO::Found 0 missing values.
2024-08-14 21:17:51.745964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.746484 INFO::Done
2024-08-14 21:17:51.76144 INFO::Formatting Data.
2024-08-14 21:17:51.762113 INFO::Recognized SummarizedExperiment
2024-08-14 21:17:51.762652 INFO::Typecasting input to dataframe.
2024-08-14 21:17:51.779985 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.781222 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.7845 INFO::Found 0 missing values.
2024-08-14 21:17:51.794457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.795031 INFO::Done
2024-08-14 21:17:51.80906 INFO::Formatting Data.
2024-08-14 21:17:51.80971 INFO::Recognized SummarizedExperiment
2024-08-14 21:17:51.810207 INFO::Typecasting input to dataframe.
2024-08-14 21:17:51.825986 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.826936 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.827915 INFO::Found 0 missing values.
2024-08-14 21:17:51.828739 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.
2024-08-14 21:17:51.832829 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.833339 INFO::Done
2024-08-14 21:17:51.84319 INFO::Formatting Data.
2024-08-14 21:17:51.843879 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.844683 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.845663 INFO::Found 0 missing values.
2024-08-14 21:17:51.848333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.848811 INFO::Done
2024-08-14 21:17:51.859591 INFO::Formatting Data.
2024-08-14 21:17:51.860286 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.861069 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.86198 INFO::Found 0 missing values.
2024-08-14 21:17:51.864902 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.865483 INFO::Done
2024-08-14 21:17:51.892321 INFO::Formatting Data.
2024-08-14 21:17:51.893171 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.8942 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.895346 INFO::Found 1 missing values.
2024-08-14 21:17:51.897827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.898345 INFO::Done
2024-08-14 21:17:51.914931 INFO::Formatting Data.
2024-08-14 21:17:51.915651 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.916458 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.917351 INFO::Found 2 missing values.
2024-08-14 21:17:51.918189 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.
2024-08-14 21:17:51.920412 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.920891 INFO::Done
2024-08-14 21:17:51.929633 INFO::Formatting Data.
2024-08-14 21:17:51.930316 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.931114 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.931988 INFO::Found 2 missing values.
2024-08-14 21:17:51.933557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.934065 INFO::Done
2024-08-14 21:17:51.943575 INFO::Formatting Data.
2024-08-14 21:17:51.944258 INFO::Typecasting input to dataframe.
2024-08-14 21:17:51.945094 INFO::Replacing NaNs with NAs.
2024-08-14 21:17:51.945925 INFO::Removing potential empty rows and columns
2024-08-14 21:17:51.946912 INFO::Found 0 missing values.
2024-08-14 21:17:51.949727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-08-14 21:17:51.950217 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.302 4.140 21.015
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.395 | 1.457 | 19.365 | |
| compute_asw | 0.025 | 0.000 | 0.025 | |
| count_existing | 0.011 | 0.004 | 0.014 | |
| generate_data_covariables | 0.009 | 0.004 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.011 | |