Yannis Schumann
| Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 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 2024-07-12 17:39 -0400 (Fri, 12 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" | 4741 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.0.0 |
| Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-07-11 22:07:35 -0400 (Thu, 11 Jul 2024) |
| EndedAt: 2024-07-11 22:09:54 -0400 (Thu, 11 Jul 2024) |
| EllapsedTime: 139.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.0.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BERT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.03 0.43 19.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2024-07-11 22:08:41.038235 INFO::Formatting Data.
2024-07-11 22:08:41.040432 INFO::Replacing NaNs with NAs.
2024-07-11 22:08:41.049509 INFO::Removing potential empty rows and columns
2024-07-11 22:08:41.482141 INFO::Found 0 missing values.
2024-07-11 22:08:41.485459 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:08:41.486326 INFO::Done
2024-07-11 22:08:41.487074 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:08:41.505167 INFO::Starting hierarchical adjustment
2024-07-11 22:08:41.506918 INFO::Found 3 batches.
2024-07-11 22:08:41.508246 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:08:41.510262 INFO::Using default BPPARAM
2024-07-11 22:08:41.511461 INFO::Processing subtree level 1
2024-07-11 22:08:44.226182 INFO::Adjusting the last 1 batches sequentially
2024-07-11 22:08:44.22818 INFO::Done
2024-07-11 22:08:44.229455 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:08:44.232739 INFO::ASW Batch was -0.0951631154938291 prior to batch effect correction and is now -0.0951631154938291 .
2024-07-11 22:08:44.234487 INFO::Total function execution time is 3.19659018516541 s and adjustment time is 2.72155904769897 s ( 85.14 )
2024-07-11 22:08:44.258234 INFO::Formatting Data.
2024-07-11 22:08:44.259801 INFO::Replacing NaNs with NAs.
2024-07-11 22:08:44.261615 INFO::Removing potential empty rows and columns
2024-07-11 22:08:44.263517 INFO::Found 0 missing values.
2024-07-11 22:08:44.265251 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.
2024-07-11 22:08:44.279916 INFO::Formatting Data.
2024-07-11 22:08:44.28145 INFO::Replacing NaNs with NAs.
2024-07-11 22:08:44.283196 INFO::Removing potential empty rows and columns
2024-07-11 22:08:44.28507 INFO::Found 0 missing values.
2024-07-11 22:08:44.286802 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.
2024-07-11 22:08:44.313087 INFO::Formatting Data.
2024-07-11 22:08:44.314597 INFO::Replacing NaNs with NAs.
2024-07-11 22:08:44.316306 INFO::Removing potential empty rows and columns
2024-07-11 22:08:44.318207 INFO::Found 0 missing values.
2024-07-11 22:08:44.319896 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.
2024-07-11 22:08:44.326234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:08:44.327548 INFO::Done
2024-07-11 22:08:44.328764 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:08:44.331963 INFO::Starting hierarchical adjustment
2024-07-11 22:08:44.333349 INFO::Found 2 batches.
2024-07-11 22:08:44.334582 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:08:44.335843 INFO::Using default BPPARAM
2024-07-11 22:08:44.337022 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:08:44.338814 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:08:44.365792 INFO::Done
2024-07-11 22:08:44.367165 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:08:44.370509 INFO::ASW Batch was -0.0543479217790527 prior to batch effect correction and is now -0.119182052952871 .
2024-07-11 22:08:44.372115 INFO::Total function execution time is 0.059114933013916 s and adjustment time is 0.0326111316680908 s ( 55.17 )
2024-07-11 22:08:44.376552 INFO::Formatting Data.
2024-07-11 22:08:44.377997 INFO::Replacing NaNs with NAs.
2024-07-11 22:08:44.390068 INFO::Formatting Data.
2024-07-11 22:08:44.39161 INFO::Replacing NaNs with NAs.
2024-07-11 22:08:44.3934 INFO::Removing potential empty rows and columns
2024-07-11 22:08:44.395293 INFO::Found 0 missing values.
2024-07-11 22:08:44.399779 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:08:44.401082 INFO::Done
2024-07-11 22:08:44.402328 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:08:44.405873 INFO::Starting hierarchical adjustment
2024-07-11 22:08:44.407318 INFO::Found 2 batches.
2024-07-11 22:08:44.408509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:08:44.409803 INFO::Using default BPPARAM
2024-07-11 22:08:44.410929 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:08:44.412614 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:08:44.433193 INFO::Done
2024-07-11 22:08:44.434649 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:08:44.438061 INFO::ASW Batch was 0.11590362031944 prior to batch effect correction and is now -0.0975211856345181 .
2024-07-11 22:08:44.439629 INFO::Total function execution time is 0.0496261119842529 s and adjustment time is 0.0260357856750488 s ( 52.46 )
2024-07-11 22:08:44.441627 INFO::Formatting Data.
2024-07-11 22:08:44.442927 INFO::Replacing NaNs with NAs.
2024-07-11 22:08:44.444571 INFO::Removing potential empty rows and columns
2024-07-11 22:08:44.446392 INFO::Found 0 missing values.
2024-07-11 22:08:44.450761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:08:44.451964 INFO::Done
2024-07-11 22:08:44.453099 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:08:44.456307 INFO::Starting hierarchical adjustment
2024-07-11 22:08:44.457676 INFO::Found 2 batches.
2024-07-11 22:08:44.458824 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:08:44.460028 INFO::Using default BPPARAM
2024-07-11 22:08:44.461186 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:08:44.462992 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:08:44.482784 INFO::Done
2024-07-11 22:08:44.484114 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:08:44.487299 INFO::ASW Batch was 0.11590362031944 prior to batch effect correction and is now -0.0975211856345181 .
2024-07-11 22:08:44.488769 INFO::Total function execution time is 0.0471739768981934 s and adjustment time is 0.0252768993377686 s ( 53.58 )
2024-07-11 22:08:47.59622 INFO::Formatting Data.
2024-07-11 22:08:47.597285 INFO::Recognized SummarizedExperiment
2024-07-11 22:08:47.598099 INFO::Typecasting input to dataframe.
2024-07-11 22:08:47.63003 INFO::Replacing NaNs with NAs.
2024-07-11 22:08:47.631534 INFO::Removing potential empty rows and columns
2024-07-11 22:08:47.634779 INFO::Found 0 missing values.
2024-07-11 22:08:47.640532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:08:47.64166 INFO::Done
2024-07-11 22:08:47.642477 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:08:47.646563 INFO::Starting hierarchical adjustment
2024-07-11 22:08:47.647522 INFO::Found 2 batches.
2024-07-11 22:08:47.648242 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:08:47.649575 INFO::Using default BPPARAM
2024-07-11 22:08:47.650321 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:08:47.651544 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:08:47.706549 INFO::Done
2024-07-11 22:08:47.708136 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:08:47.714738 INFO::ASW Batch was 0.0188043180719327 prior to batch effect correction and is now -0.102110688447012 .
2024-07-11 22:08:47.716608 INFO::Total function execution time is 0.120541095733643 s and adjustment time is 0.0590360164642334 s ( 48.98 )
2024-07-11 22:08:47.748796 INFO::Formatting Data.
2024-07-11 22:08:47.750398 INFO::Recognized SummarizedExperiment
2024-07-11 22:08:47.751804 INFO::Typecasting input to dataframe.
2024-07-11 22:08:47.766096 INFO::Replacing NaNs with NAs.
2024-07-11 22:08:47.768457 INFO::Removing potential empty rows and columns
2024-07-11 22:08:47.774034 INFO::Found 0 missing values.
2024-07-11 22:08:47.785116 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:08:47.786684 INFO::Done
2024-07-11 22:08:47.788095 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:08:47.795007 INFO::Starting hierarchical adjustment
2024-07-11 22:08:47.796858 INFO::Found 2 batches.
2024-07-11 22:08:47.798285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:08:47.799785 INFO::Using default BPPARAM
2024-07-11 22:08:47.801136 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:08:47.80333 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:08:47.842086 INFO::Done
2024-07-11 22:08:47.843727 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:08:47.850593 INFO::ASW Batch was -0.0116657579123331 prior to batch effect correction and is now -0.0116657579123331 .
2024-07-11 22:08:47.852526 INFO::Total function execution time is 0.103667974472046 s and adjustment time is 0.0454769134521484 s ( 43.87 )
2024-07-11 22:08:47.888288 INFO::Formatting Data.
2024-07-11 22:08:47.890004 INFO::Replacing NaNs with NAs.
2024-07-11 22:08:47.89191 INFO::Removing potential empty rows and columns
2024-07-11 22:08:47.894037 INFO::Found 0 missing values.
2024-07-11 22:08:47.899111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:08:47.900472 INFO::Done
2024-07-11 22:08:47.901837 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:08:47.905555 INFO::Starting hierarchical adjustment
2024-07-11 22:08:47.907191 INFO::Found 3 batches.
2024-07-11 22:08:47.908577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:08:47.910039 INFO::Using default BPPARAM
2024-07-11 22:08:47.911335 INFO::Processing subtree level 1
2024-07-11 22:08:58.410012 INFO::Adjusting the last 1 batches sequentially
2024-07-11 22:08:58.412406 INFO::Done
2024-07-11 22:08:58.413817 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:08:58.417052 INFO::ASW Batch was -0.0474525881435912 prior to batch effect correction and is now -0.186150149636614 .
2024-07-11 22:08:58.418642 INFO::Total function execution time is 10.5304780006409 s and adjustment time is 10.5054450035095 s ( 99.76 )
2024-07-11 22:08:58.442073 INFO::Skipping initial DF formatting
2024-07-11 22:08:58.443485 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:08:58.449623 INFO::Starting hierarchical adjustment
2024-07-11 22:08:58.451053 INFO::Found 5 batches.
2024-07-11 22:08:58.452165 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:08:58.453334 INFO::Using default BPPARAM
2024-07-11 22:08:58.454396 INFO::Processing subtree level 1
2024-07-11 22:09:01.263362 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:01.265424 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:01.286199 INFO::Done
2024-07-11 22:09:01.287114 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:01.291586 INFO::ASW Batch was 0.486455835174312 prior to batch effect correction and is now 0.486455835174312 .
2024-07-11 22:09:01.292446 INFO::ASW Label was 0.394848877699158 prior to batch effect correction and is now 0.394848877699158 .
2024-07-11 22:09:01.293415 INFO::Total function execution time is 2.85155510902405 s and adjustment time is 2.83537006378174 s ( 99.43 )
2024-07-11 22:09:01.314171 INFO::Formatting Data.
2024-07-11 22:09:01.315201 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:01.316283 INFO::Removing potential empty rows and columns
2024-07-11 22:09:01.317398 INFO::Found 0 missing values.
2024-07-11 22:09:01.321177 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:01.321936 INFO::Done
2024-07-11 22:09:01.322665 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:01.326022 INFO::Starting hierarchical adjustment
2024-07-11 22:09:01.326961 INFO::Found 5 batches.
2024-07-11 22:09:01.327731 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:01.328513 INFO::Using default BPPARAM
2024-07-11 22:09:01.32921 INFO::Processing subtree level 1
2024-07-11 22:09:04.482267 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:04.484204 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:04.498379 INFO::Done
2024-07-11 22:09:04.499321 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:04.502458 INFO::ASW Batch was 0.287995775227134 prior to batch effect correction and is now -0.0820662940769562 .
2024-07-11 22:09:04.50386 INFO::ASW Label was 0.399807620267377 prior to batch effect correction and is now 0.787496214972352 .
2024-07-11 22:09:04.505526 INFO::Total function execution time is 3.19140195846558 s and adjustment time is 3.17152500152588 s ( 99.38 )
2024-07-11 22:09:04.507187 INFO::Formatting Data.
2024-07-11 22:09:04.508605 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:04.510399 INFO::Removing potential empty rows and columns
2024-07-11 22:09:04.511755 INFO::Found 0 missing values.
2024-07-11 22:09:04.515407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:04.516151 INFO::Done
2024-07-11 22:09:04.516847 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:04.520007 INFO::Starting hierarchical adjustment
2024-07-11 22:09:04.52091 INFO::Found 5 batches.
2024-07-11 22:09:04.521676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:04.522472 INFO::Using default BPPARAM
2024-07-11 22:09:04.523166 INFO::Processing subtree level 1
2024-07-11 22:09:07.568474 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:07.570189 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:07.581867 INFO::Done
2024-07-11 22:09:07.582739 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:07.585868 INFO::ASW Batch was 0.287995775227134 prior to batch effect correction and is now -0.0820662940769562 .
2024-07-11 22:09:07.586647 INFO::ASW Label was 0.399807620267377 prior to batch effect correction and is now 0.787496214972352 .
2024-07-11 22:09:07.58766 INFO::Total function execution time is 3.08054709434509 s and adjustment time is 3.06107091903687 s ( 99.37 )
2024-07-11 22:09:07.605108 INFO::Formatting Data.
2024-07-11 22:09:07.606205 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:07.6074 INFO::Removing potential empty rows and columns
2024-07-11 22:09:07.608625 INFO::Found 0 missing values.
2024-07-11 22:09:07.61218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:07.612934 INFO::Done
2024-07-11 22:09:07.613643 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:07.616618 INFO::Starting hierarchical adjustment
2024-07-11 22:09:07.617512 INFO::Found 5 batches.
2024-07-11 22:09:07.618219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:07.619233 INFO::Using default BPPARAM
2024-07-11 22:09:07.619977 INFO::Processing subtree level 1
2024-07-11 22:09:10.716735 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:10.718775 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:10.736155 INFO::Done
2024-07-11 22:09:10.737498 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:10.741913 INFO::ASW Batch was 0.296660199901086 prior to batch effect correction and is now -0.0764735454268093 .
2024-07-11 22:09:10.743068 INFO::ASW Label was 0.460354748718727 prior to batch effect correction and is now 0.779054255964281 .
2024-07-11 22:09:10.744064 INFO::Total function execution time is 3.13905620574951 s and adjustment time is 3.11869597434998 s ( 99.35 )
2024-07-11 22:09:10.745127 INFO::Formatting Data.
2024-07-11 22:09:10.746129 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:10.747725 INFO::Removing potential empty rows and columns
2024-07-11 22:09:10.749435 INFO::Found 0 missing values.
2024-07-11 22:09:10.755296 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:10.756539 INFO::Done
2024-07-11 22:09:10.757733 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:10.761901 INFO::Starting hierarchical adjustment
2024-07-11 22:09:10.762845 INFO::Found 5 batches.
2024-07-11 22:09:10.763583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:10.764373 INFO::Using default BPPARAM
2024-07-11 22:09:10.765061 INFO::Processing subtree level 1
2024-07-11 22:09:13.814985 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:13.816527 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:13.833983 INFO::Done
2024-07-11 22:09:13.835372 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:13.839873 INFO::ASW Batch was 0.296660199901086 prior to batch effect correction and is now -0.0764735454268093 .
2024-07-11 22:09:13.841183 INFO::ASW Label was 0.460354748718727 prior to batch effect correction and is now 0.779054255964281 .
2024-07-11 22:09:13.84271 INFO::Total function execution time is 3.09756994247437 s and adjustment time is 3.07119607925415 s ( 99.15 )
2024-07-11 22:09:13.865297 INFO::Formatting Data.
2024-07-11 22:09:13.866793 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:13.868478 INFO::Removing potential empty rows and columns
2024-07-11 22:09:13.870259 INFO::Found 0 missing values.
2024-07-11 22:09:13.874041 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:13.875264 INFO::Done
2024-07-11 22:09:13.876406 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:13.880772 INFO::Starting hierarchical adjustment
2024-07-11 22:09:13.882206 INFO::Found 2 batches.
2024-07-11 22:09:13.883349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:13.884563 INFO::Using default BPPARAM
2024-07-11 22:09:13.885684 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:13.887389 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:13.902316 INFO::Done
2024-07-11 22:09:13.90326 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:13.906263 INFO::ASW Batch was 0.35540221088308 prior to batch effect correction and is now -0.0336324387795297 .
2024-07-11 22:09:13.907083 INFO::ASW Label was 0.621870480328492 prior to batch effect correction and is now 0.892251074735444 .
2024-07-11 22:09:13.908022 INFO::Total function execution time is 0.0429160594940186 s and adjustment time is 0.0203151702880859 s ( 47.34 )
2024-07-11 22:09:13.908975 INFO::Formatting Data.
2024-07-11 22:09:13.909779 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:13.910832 INFO::Removing potential empty rows and columns
2024-07-11 22:09:13.912262 INFO::Found 0 missing values.
2024-07-11 22:09:13.915984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:13.916759 INFO::Done
2024-07-11 22:09:13.91746 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:13.920683 INFO::Starting hierarchical adjustment
2024-07-11 22:09:13.921687 INFO::Found 2 batches.
2024-07-11 22:09:13.922487 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:13.923338 INFO::Using default BPPARAM
2024-07-11 22:09:13.924054 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:13.9252 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:13.937469 INFO::Done
2024-07-11 22:09:13.938375 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:13.941505 INFO::ASW Batch was 0.35540221088308 prior to batch effect correction and is now -0.0336324387795297 .
2024-07-11 22:09:13.942321 INFO::ASW Label was 0.621870480328492 prior to batch effect correction and is now 0.892251074735444 .
2024-07-11 22:09:13.943308 INFO::Total function execution time is 0.0343601703643799 s and adjustment time is 0.0159189701080322 s ( 46.33 )
2024-07-11 22:09:13.958301 INFO::Formatting Data.
2024-07-11 22:09:13.959322 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:13.960456 INFO::Removing potential empty rows and columns
2024-07-11 22:09:13.961506 INFO::Found 0 missing values.
2024-07-11 22:09:13.963549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:13.964274 INFO::Done
2024-07-11 22:09:13.964956 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:13.967049 INFO::Starting hierarchical adjustment
2024-07-11 22:09:13.968021 INFO::Found 2 batches.
2024-07-11 22:09:13.968728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:13.969505 INFO::Using default BPPARAM
2024-07-11 22:09:13.970218 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:13.971275 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:13.997088 INFO::Done
2024-07-11 22:09:13.997983 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:14.000048 INFO::ASW Batch was -0.0829075843422107 prior to batch effect correction and is now -0.130451986753957 .
2024-07-11 22:09:14.00107 INFO::Total function execution time is 0.0428669452667236 s and adjustment time is 0.0291669368743896 s ( 68.04 )
2024-07-11 22:09:14.01979 INFO::Formatting Data.
2024-07-11 22:09:14.021431 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:14.023198 INFO::Removing potential empty rows and columns
2024-07-11 22:09:14.024405 INFO::Found 0 missing values.
2024-07-11 22:09:14.025655 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.
2024-07-11 22:09:14.02977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:14.031049 INFO::Done
2024-07-11 22:09:14.032221 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:14.035324 INFO::Starting hierarchical adjustment
2024-07-11 22:09:14.036229 INFO::Found 2 batches.
2024-07-11 22:09:14.036943 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:14.037717 INFO::Using default BPPARAM
2024-07-11 22:09:14.038447 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:14.039565 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:14.053324 INFO::Done
2024-07-11 22:09:14.054219 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:14.057195 INFO::ASW Batch was 0.355678272582107 prior to batch effect correction and is now -0.0370464223814968 .
2024-07-11 22:09:14.058007 INFO::ASW Label was 0.662893825408533 prior to batch effect correction and is now 0.943386936710472 .
2024-07-11 22:09:14.05899 INFO::Total function execution time is 0.0393970012664795 s and adjustment time is 0.0171890258789062 s ( 43.63 )
2024-07-11 22:09:14.059986 INFO::Formatting Data.
2024-07-11 22:09:14.060806 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:14.061878 INFO::Removing potential empty rows and columns
2024-07-11 22:09:14.063032 INFO::Found 0 missing values.
2024-07-11 22:09:14.064158 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.
2024-07-11 22:09:14.068072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:14.068877 INFO::Done
2024-07-11 22:09:14.06958 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:14.072692 INFO::Starting hierarchical adjustment
2024-07-11 22:09:14.073622 INFO::Found 2 batches.
2024-07-11 22:09:14.074337 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:14.075221 INFO::Using default BPPARAM
2024-07-11 22:09:14.075929 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:14.077077 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:14.09214 INFO::Done
2024-07-11 22:09:14.093032 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:14.096162 INFO::ASW Batch was 0.355678272582107 prior to batch effect correction and is now -0.0370464223814968 .
2024-07-11 22:09:14.096993 INFO::ASW Label was 0.662893825408533 prior to batch effect correction and is now 0.943386936710472 .
2024-07-11 22:09:14.097979 INFO::Total function execution time is 0.0380001068115234 s and adjustment time is 0.0186319351196289 s ( 49.03 )
2024-07-11 22:09:14.351738 INFO::Formatting Data.
2024-07-11 22:09:14.353332 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:14.355094 INFO::Removing potential empty rows and columns
2024-07-11 22:09:14.35704 INFO::Found 0 missing values.
2024-07-11 22:09:14.361663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:14.362865 INFO::Done
2024-07-11 22:09:14.364015 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:14.367281 INFO::Starting hierarchical adjustment
2024-07-11 22:09:14.368669 INFO::Found 3 batches.
2024-07-11 22:09:14.369796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:14.371068 INFO::Using default BPPARAM
2024-07-11 22:09:14.372261 INFO::Processing subtree level 1
2024-07-11 22:09:17.158891 INFO::Adjusting the last 1 batches sequentially
2024-07-11 22:09:17.161135 INFO::Done
2024-07-11 22:09:17.162476 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:17.165586 INFO::ASW Batch was -0.0172480157721016 prior to batch effect correction and is now -0.0172480157721016 .
2024-07-11 22:09:17.167119 INFO::Total function execution time is 2.81552004814148 s and adjustment time is 2.79267287254333 s ( 99.19 )
2024-07-11 22:09:17.168798 INFO::Formatting Data.
2024-07-11 22:09:17.17008 INFO::Typecasting input to dataframe.
2024-07-11 22:09:17.171482 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:17.172968 INFO::Removing potential empty rows and columns
2024-07-11 22:09:17.174565 INFO::Found 0 missing values.
2024-07-11 22:09:17.178432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:17.179168 INFO::Done
2024-07-11 22:09:17.179858 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:17.181878 INFO::Starting hierarchical adjustment
2024-07-11 22:09:17.18288 INFO::Found 3 batches.
2024-07-11 22:09:17.183659 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:17.184467 INFO::Using default BPPARAM
2024-07-11 22:09:17.18517 INFO::Processing subtree level 1
2024-07-11 22:09:20.045153 INFO::Adjusting the last 1 batches sequentially
2024-07-11 22:09:20.046723 INFO::Done
2024-07-11 22:09:20.047563 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:20.049703 INFO::ASW Batch was -0.0172480157721016 prior to batch effect correction and is now -0.0172480157721016 .
2024-07-11 22:09:20.050678 INFO::Total function execution time is 2.88198089599609 s and adjustment time is 2.86394786834717 s ( 99.37 )
2024-07-11 22:09:20.066046 INFO::Formatting Data.
2024-07-11 22:09:20.067047 INFO::Typecasting input to dataframe.
2024-07-11 22:09:20.068057 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:20.069168 INFO::Removing potential empty rows and columns
2024-07-11 22:09:20.070295 INFO::Found 0 missing values.
2024-07-11 22:09:20.072964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:20.073761 INFO::Done
2024-07-11 22:09:20.074537 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:20.076671 INFO::Starting hierarchical adjustment
2024-07-11 22:09:20.077536 INFO::Found 3 batches.
2024-07-11 22:09:20.07842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:20.079597 INFO::Using default BPPARAM
2024-07-11 22:09:20.080763 INFO::Processing subtree level 1
2024-07-11 22:09:23.095842 INFO::Adjusting the last 1 batches sequentially
2024-07-11 22:09:23.09838 INFO::Done
2024-07-11 22:09:23.099898 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:23.103527 INFO::ASW Batch was -0.0739756462496305 prior to batch effect correction and is now -0.0739756462496305 .
2024-07-11 22:09:23.105371 INFO::Total function execution time is 3.03927302360535 s and adjustment time is 3.0208899974823 s ( 99.4 )
2024-07-11 22:09:26.580848 INFO::Formatting Data.
2024-07-11 22:09:26.582707 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:26.585216 INFO::Removing potential empty rows and columns
2024-07-11 22:09:26.589605 INFO::Found 1000 missing values.
2024-07-11 22:09:26.615516 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:26.617137 INFO::Done
2024-07-11 22:09:26.618691 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:26.629534 INFO::Starting hierarchical adjustment
2024-07-11 22:09:26.631365 INFO::Found 10 batches.
2024-07-11 22:09:26.632776 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:26.634224 INFO::Using default BPPARAM
2024-07-11 22:09:26.635513 INFO::Processing subtree level 1
2024-07-11 22:09:30.203275 INFO::Processing subtree level 2
2024-07-11 22:09:33.127881 INFO::Adjusting the last 1 batches sequentially
2024-07-11 22:09:33.130369 INFO::Done
2024-07-11 22:09:33.13162 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:33.146118 INFO::ASW Batch was 0.488082269701411 prior to batch effect correction and is now 0.488082269701411 .
2024-07-11 22:09:33.147619 INFO::ASW Label was 0.330996333781753 prior to batch effect correction and is now 0.330996333781753 .
2024-07-11 22:09:33.149212 INFO::Total function execution time is 6.56855201721191 s and adjustment time is 6.49931693077087 s ( 98.95 )
2024-07-11 22:09:33.151029 INFO::Formatting Data.
2024-07-11 22:09:33.152344 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:33.154269 INFO::Removing potential empty rows and columns
2024-07-11 22:09:33.157434 INFO::Found 1000 missing values.
2024-07-11 22:09:33.181935 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:33.183904 INFO::Done
2024-07-11 22:09:33.1854 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:33.193768 INFO::Starting hierarchical adjustment
2024-07-11 22:09:33.194978 INFO::Found 10 batches.
2024-07-11 22:09:33.938599 INFO::Set up parallel execution backend with 2 workers
2024-07-11 22:09:33.940108 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-11 22:09:36.813857 INFO::Adjusting the last 2 batches sequentially
2024-07-11 22:09:36.81638 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-11 22:09:36.841946 INFO::Done
2024-07-11 22:09:36.843578 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:36.853846 INFO::ASW Batch was 0.488082269701411 prior to batch effect correction and is now 0.488082269701411 .
2024-07-11 22:09:36.855491 INFO::ASW Label was 0.330996333781753 prior to batch effect correction and is now 0.330996333781753 .
2024-07-11 22:09:36.857342 INFO::Total function execution time is 3.70641899108887 s and adjustment time is 3.64705014228821 s ( 98.4 )
2024-07-11 22:09:39.802895 INFO::Formatting Data.
2024-07-11 22:09:39.804473 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:39.806196 INFO::Removing potential empty rows and columns
2024-07-11 22:09:39.80803 INFO::Found 0 missing values.
2024-07-11 22:09:39.813245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:39.814525 INFO::Done
2024-07-11 22:09:39.815585 INFO::Acquiring quality metrics before batch effect correction.
2024-07-11 22:09:39.818561 INFO::Starting hierarchical adjustment
2024-07-11 22:09:39.819527 INFO::Found 3 batches.
2024-07-11 22:09:39.820368 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-11 22:09:39.821162 INFO::Using default BPPARAM
2024-07-11 22:09:39.821954 INFO::Processing subtree level 1
2024-07-11 22:09:42.74987 INFO::Adjusting the last 1 batches sequentially
2024-07-11 22:09:42.752275 INFO::Done
2024-07-11 22:09:42.753723 INFO::Acquiring quality metrics after batch effect correction.
2024-07-11 22:09:42.758146 INFO::ASW Batch was 0.208609873405118 prior to batch effect correction and is now -0.131453661358569 .
2024-07-11 22:09:42.759463 INFO::ASW Label was -0.186797212103199 prior to batch effect correction and is now -0.014619504121269 .
2024-07-11 22:09:42.761037 INFO::Total function execution time is 2.95822691917419 s and adjustment time is 2.93285179138184 s ( 99.14 )
2024-07-11 22:09:42.959223 INFO::Formatting Data.
2024-07-11 22:09:42.96087 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:42.962668 INFO::Removing potential empty rows and columns
2024-07-11 22:09:42.964472 INFO::Found 2 missing values.
2024-07-11 22:09:42.968644 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:42.969896 INFO::Done
2024-07-11 22:09:43.02819 INFO::Found NA in Reference column
2024-07-11 22:09:43.047898 INFO::Require at least two references per batch.
2024-07-11 22:09:43.080307 INFO::Formatting Data.
2024-07-11 22:09:43.081918 INFO::Recognized SummarizedExperiment
2024-07-11 22:09:43.083363 INFO::Typecasting input to dataframe.
2024-07-11 22:09:43.097113 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:43.099218 INFO::Removing potential empty rows and columns
2024-07-11 22:09:43.104281 INFO::Found 0 missing values.
2024-07-11 22:09:43.113614 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:43.115064 INFO::Done
2024-07-11 22:09:43.139275 INFO::Formatting Data.
2024-07-11 22:09:43.140819 INFO::Recognized SummarizedExperiment
2024-07-11 22:09:43.142122 INFO::Typecasting input to dataframe.
2024-07-11 22:09:43.167972 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:43.17018 INFO::Removing potential empty rows and columns
2024-07-11 22:09:43.175533 INFO::Found 0 missing values.
2024-07-11 22:09:43.190858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:43.192297 INFO::Done
2024-07-11 22:09:43.216041 INFO::Formatting Data.
2024-07-11 22:09:43.21703 INFO::Recognized SummarizedExperiment
2024-07-11 22:09:43.217824 INFO::Typecasting input to dataframe.
2024-07-11 22:09:43.232945 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:43.234198 INFO::Removing potential empty rows and columns
2024-07-11 22:09:43.235363 INFO::Found 0 missing values.
2024-07-11 22:09:43.236446 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.
2024-07-11 22:09:43.240184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:43.240938 INFO::Done
2024-07-11 22:09:43.259465 INFO::Formatting Data.
2024-07-11 22:09:43.260513 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:43.261648 INFO::Removing potential empty rows and columns
2024-07-11 22:09:43.262785 INFO::Found 0 missing values.
2024-07-11 22:09:43.265385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:43.266109 INFO::Done
2024-07-11 22:09:43.282492 INFO::Formatting Data.
2024-07-11 22:09:43.284178 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:43.285931 INFO::Removing potential empty rows and columns
2024-07-11 22:09:43.287099 INFO::Found 0 missing values.
2024-07-11 22:09:43.289709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:43.290439 INFO::Done
2024-07-11 22:09:43.334389 INFO::Formatting Data.
2024-07-11 22:09:43.335428 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:43.336698 INFO::Removing potential empty rows and columns
2024-07-11 22:09:43.337967 INFO::Found 1 missing values.
2024-07-11 22:09:43.340498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:43.341283 INFO::Done
2024-07-11 22:09:43.365997 INFO::Formatting Data.
2024-07-11 22:09:43.367067 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:43.368175 INFO::Removing potential empty rows and columns
2024-07-11 22:09:43.369287 INFO::Found 2 missing values.
2024-07-11 22:09:43.370398 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.
2024-07-11 22:09:43.372559 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:43.373274 INFO::Done
2024-07-11 22:09:43.387258 INFO::Formatting Data.
2024-07-11 22:09:43.388314 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:43.389385 INFO::Removing potential empty rows and columns
2024-07-11 22:09:43.390436 INFO::Found 2 missing values.
2024-07-11 22:09:43.392047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:43.392761 INFO::Done
2024-07-11 22:09:43.410311 INFO::Formatting Data.
2024-07-11 22:09:43.411345 INFO::Typecasting input to dataframe.
2024-07-11 22:09:43.412369 INFO::Replacing NaNs with NAs.
2024-07-11 22:09:43.413424 INFO::Removing potential empty rows and columns
2024-07-11 22:09:43.414559 INFO::Found 0 missing values.
2024-07-11 22:09:43.41718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-11 22:09:43.417921 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
31.07 1.37 79.73
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.03 | 0.43 | 19.16 | |
| compute_asw | 0.03 | 0.00 | 0.03 | |
| count_existing | 0.02 | 0.00 | 0.01 | |
| generate_data_covariables | 0.01 | 0.00 | 0.02 | |
| generate_dataset | 0.02 | 0.00 | 0.01 | |