Yannis Schumann
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.2.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2024-12-19 23:12:21 -0500 (Thu, 19 Dec 2024) |
| EndedAt: 2024-12-19 23:14:39 -0500 (Thu, 19 Dec 2024) |
| EllapsedTime: 138.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '1.2.0'
* 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 8.94 0.69 18.63
* 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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")
2024-12-19 23:13:25.485354 INFO::Formatting Data.
2024-12-19 23:13:25.487522 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:25.496483 INFO::Removing potential empty rows and columns
2024-12-19 23:13:25.748572 INFO::Found 0 missing values.
2024-12-19 23:13:25.751778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:25.752663 INFO::Done
2024-12-19 23:13:25.753406 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:25.769291 INFO::Starting hierarchical adjustment
2024-12-19 23:13:25.770368 INFO::Found 3 batches.
2024-12-19 23:13:25.771097 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:25.772403 INFO::Using default BPPARAM
2024-12-19 23:13:25.773145 INFO::Processing subtree level 1
2024-12-19 23:13:28.276828 INFO::Adjusting the last 1 batches sequentially
2024-12-19 23:13:28.279229 INFO::Done
2024-12-19 23:13:28.280549 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:28.283803 INFO::ASW Batch was -0.116627620405141 prior to batch effect correction and is now -0.116627620405141 .
2024-12-19 23:13:28.285515 INFO::Total function execution time is 2.80051183700562 s and adjustment time is 2.50897812843323 s ( 89.59 )
2024-12-19 23:13:28.307299 INFO::Formatting Data.
2024-12-19 23:13:28.308866 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:28.310725 INFO::Removing potential empty rows and columns
2024-12-19 23:13:28.312709 INFO::Found 0 missing values.
2024-12-19 23:13:28.314312 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.
2024-12-19 23:13:28.326692 INFO::Formatting Data.
2024-12-19 23:13:28.327804 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:28.328869 INFO::Removing potential empty rows and columns
2024-12-19 23:13:28.329981 INFO::Found 0 missing values.
2024-12-19 23:13:28.331048 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.
2024-12-19 23:13:28.346675 INFO::Formatting Data.
2024-12-19 23:13:28.347641 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:28.348676 INFO::Removing potential empty rows and columns
2024-12-19 23:13:28.349788 INFO::Found 0 missing values.
2024-12-19 23:13:28.350857 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.
2024-12-19 23:13:28.354606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:28.35533 INFO::Done
2024-12-19 23:13:28.356014 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:28.358069 INFO::Starting hierarchical adjustment
2024-12-19 23:13:28.358922 INFO::Found 2 batches.
2024-12-19 23:13:28.359702 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:28.36048 INFO::Using default BPPARAM
2024-12-19 23:13:28.361182 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:13:28.36224 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:13:28.378606 INFO::Done
2024-12-19 23:13:28.379486 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:28.38163 INFO::ASW Batch was -0.025659425931042 prior to batch effect correction and is now -0.114247105837441 .
2024-12-19 23:13:28.382631 INFO::Total function execution time is 0.0360479354858398 s and adjustment time is 0.0197720527648926 s ( 54.85 )
2024-12-19 23:13:28.386291 INFO::Formatting Data.
2024-12-19 23:13:28.387108 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:28.394001 INFO::Formatting Data.
2024-12-19 23:13:28.39483 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:28.395819 INFO::Removing potential empty rows and columns
2024-12-19 23:13:28.396886 INFO::Found 0 missing values.
2024-12-19 23:13:28.399401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:28.400344 INFO::Done
2024-12-19 23:13:28.401387 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:28.404313 INFO::Starting hierarchical adjustment
2024-12-19 23:13:28.405204 INFO::Found 2 batches.
2024-12-19 23:13:28.405896 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:28.406648 INFO::Using default BPPARAM
2024-12-19 23:13:28.407332 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:13:28.408396 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:13:28.423354 INFO::Done
2024-12-19 23:13:28.424706 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:28.428073 INFO::ASW Batch was 0.106663066123953 prior to batch effect correction and is now -0.132581559368496 .
2024-12-19 23:13:28.429689 INFO::Total function execution time is 0.035599946975708 s and adjustment time is 0.0182089805603027 s ( 51.15 )
2024-12-19 23:13:28.431681 INFO::Formatting Data.
2024-12-19 23:13:28.433038 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:28.434721 INFO::Removing potential empty rows and columns
2024-12-19 23:13:28.436558 INFO::Found 0 missing values.
2024-12-19 23:13:28.440864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:28.442068 INFO::Done
2024-12-19 23:13:28.443225 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:28.446519 INFO::Starting hierarchical adjustment
2024-12-19 23:13:28.447913 INFO::Found 2 batches.
2024-12-19 23:13:28.449079 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:28.45036 INFO::Using default BPPARAM
2024-12-19 23:13:28.451495 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:13:28.453211 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:13:28.474302 INFO::Done
2024-12-19 23:13:28.475746 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:28.479252 INFO::ASW Batch was 0.106663066123953 prior to batch effect correction and is now -0.132581559368496 .
2024-12-19 23:13:28.480902 INFO::Total function execution time is 0.0492269992828369 s and adjustment time is 0.026561975479126 s ( 53.96 )
2024-12-19 23:13:31.401372 INFO::Formatting Data.
2024-12-19 23:13:31.402455 INFO::Recognized SummarizedExperiment
2024-12-19 23:13:31.403436 INFO::Typecasting input to dataframe.
2024-12-19 23:13:31.450848 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:31.453177 INFO::Removing potential empty rows and columns
2024-12-19 23:13:31.458986 INFO::Found 0 missing values.
2024-12-19 23:13:31.469211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:31.470796 INFO::Done
2024-12-19 23:13:31.472181 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:31.478874 INFO::Starting hierarchical adjustment
2024-12-19 23:13:31.480545 INFO::Found 2 batches.
2024-12-19 23:13:31.481861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:31.483966 INFO::Using default BPPARAM
2024-12-19 23:13:31.485228 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:13:31.487287 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:13:31.558901 INFO::Done
2024-12-19 23:13:31.559873 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:31.564021 INFO::ASW Batch was 0.0324753682601792 prior to batch effect correction and is now -0.0921588388730399 .
2024-12-19 23:13:31.565106 INFO::Total function execution time is 0.164009094238281 s and adjustment time is 0.0786240100860596 s ( 47.94 )
2024-12-19 23:13:32.349139 INFO::Formatting Data.
2024-12-19 23:13:32.350107 INFO::Recognized SummarizedExperiment
2024-12-19 23:13:32.350831 INFO::Typecasting input to dataframe.
2024-12-19 23:13:32.358812 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:32.360175 INFO::Removing potential empty rows and columns
2024-12-19 23:13:32.363015 INFO::Found 0 missing values.
2024-12-19 23:13:32.368132 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:32.369198 INFO::Done
2024-12-19 23:13:32.37002 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:32.37621 INFO::Starting hierarchical adjustment
2024-12-19 23:13:32.377439 INFO::Found 2 batches.
2024-12-19 23:13:32.378209 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:32.379114 INFO::Using default BPPARAM
2024-12-19 23:13:32.379894 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:13:32.381131 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:13:32.400234 INFO::Done
2024-12-19 23:13:32.401157 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:32.404991 INFO::ASW Batch was -0.0136175441631404 prior to batch effect correction and is now -0.0136175441631404 .
2024-12-19 23:13:32.406323 INFO::Total function execution time is 0.0571370124816895 s and adjustment time is 0.02292799949646 s ( 40.13 )
2024-12-19 23:13:32.434686 INFO::Formatting Data.
2024-12-19 23:13:32.436257 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:32.438038 INFO::Removing potential empty rows and columns
2024-12-19 23:13:32.439922 INFO::Found 0 missing values.
2024-12-19 23:13:32.444521 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:32.445808 INFO::Done
2024-12-19 23:13:32.447001 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:32.450371 INFO::Starting hierarchical adjustment
2024-12-19 23:13:32.451847 INFO::Found 3 batches.
2024-12-19 23:13:32.453035 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:32.454304 INFO::Using default BPPARAM
2024-12-19 23:13:32.455499 INFO::Processing subtree level 1
2024-12-19 23:13:43.562919 INFO::Adjusting the last 1 batches sequentially
2024-12-19 23:13:43.565051 INFO::Done
2024-12-19 23:13:43.565901 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:43.568141 INFO::ASW Batch was -0.0777429023102981 prior to batch effect correction and is now -0.17967501688619 .
2024-12-19 23:13:43.569167 INFO::Total function execution time is 11.1346740722656 s and adjustment time is 11.1134569644928 s ( 99.81 )
2024-12-19 23:13:43.58639 INFO::Skipping initial DF formatting
2024-12-19 23:13:43.587925 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:43.593938 INFO::Starting hierarchical adjustment
2024-12-19 23:13:43.595019 INFO::Found 5 batches.
2024-12-19 23:13:43.595834 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:43.596689 INFO::Using default BPPARAM
2024-12-19 23:13:43.597513 INFO::Processing subtree level 1
2024-12-19 23:13:46.762929 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:13:46.764527 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:13:46.779114 INFO::Done
2024-12-19 23:13:46.780004 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:46.784195 INFO::ASW Batch was 0.540758126004401 prior to batch effect correction and is now 0.540758126004401 .
2024-12-19 23:13:46.784996 INFO::ASW Label was 0.474975862568214 prior to batch effect correction and is now 0.474975862568214 .
2024-12-19 23:13:46.785942 INFO::Total function execution time is 3.19979619979858 s and adjustment time is 3.18423581123352 s ( 99.51 )
2024-12-19 23:13:46.803758 INFO::Formatting Data.
2024-12-19 23:13:46.804733 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:46.805802 INFO::Removing potential empty rows and columns
2024-12-19 23:13:46.8069 INFO::Found 0 missing values.
2024-12-19 23:13:46.810442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:46.811177 INFO::Done
2024-12-19 23:13:46.811868 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:46.814966 INFO::Starting hierarchical adjustment
2024-12-19 23:13:46.815864 INFO::Found 5 batches.
2024-12-19 23:13:46.816595 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:46.817381 INFO::Using default BPPARAM
2024-12-19 23:13:46.818084 INFO::Processing subtree level 1
2024-12-19 23:13:50.08098 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:13:50.083258 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:13:50.104725 INFO::Done
2024-12-19 23:13:50.106207 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:50.111533 INFO::ASW Batch was 0.400630468561241 prior to batch effect correction and is now -0.0309036222642698 .
2024-12-19 23:13:50.112899 INFO::ASW Label was 0.390806303629728 prior to batch effect correction and is now 0.75951882677322 .
2024-12-19 23:13:50.114428 INFO::Total function execution time is 3.31067514419556 s and adjustment time is 3.28892397880554 s ( 99.34 )
2024-12-19 23:13:50.116014 INFO::Formatting Data.
2024-12-19 23:13:50.117592 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:50.119186 INFO::Removing potential empty rows and columns
2024-12-19 23:13:50.12097 INFO::Found 0 missing values.
2024-12-19 23:13:50.127217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:50.128555 INFO::Done
2024-12-19 23:13:50.129973 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:50.135266 INFO::Starting hierarchical adjustment
2024-12-19 23:13:50.13678 INFO::Found 5 batches.
2024-12-19 23:13:50.137951 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:50.139212 INFO::Using default BPPARAM
2024-12-19 23:13:50.140596 INFO::Processing subtree level 1
2024-12-19 23:13:53.572767 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:13:53.574882 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:13:53.599658 INFO::Done
2024-12-19 23:13:53.601169 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:53.607553 INFO::ASW Batch was 0.400630468561241 prior to batch effect correction and is now -0.0309036222642698 .
2024-12-19 23:13:53.609036 INFO::ASW Label was 0.390806303629728 prior to batch effect correction and is now 0.75951882677322 .
2024-12-19 23:13:53.610797 INFO::Total function execution time is 3.49470090866089 s and adjustment time is 3.46306490898132 s ( 99.09 )
2024-12-19 23:13:53.636408 INFO::Formatting Data.
2024-12-19 23:13:53.638925 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:53.640765 INFO::Removing potential empty rows and columns
2024-12-19 23:13:53.64305 INFO::Found 0 missing values.
2024-12-19 23:13:53.649862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:53.650767 INFO::Done
2024-12-19 23:13:53.651614 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:53.655487 INFO::Starting hierarchical adjustment
2024-12-19 23:13:53.656502 INFO::Found 5 batches.
2024-12-19 23:13:53.65765 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:53.658508 INFO::Using default BPPARAM
2024-12-19 23:13:53.65929 INFO::Processing subtree level 1
2024-12-19 23:13:56.982371 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:13:56.984077 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:13:56.996251 INFO::Done
2024-12-19 23:13:56.997124 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:13:57.000964 INFO::ASW Batch was 0.490309876582596 prior to batch effect correction and is now -0.0679424319383092 .
2024-12-19 23:13:57.001762 INFO::ASW Label was 0.342868028510102 prior to batch effect correction and is now 0.724373398562586 .
2024-12-19 23:13:57.002768 INFO::Total function execution time is 3.3665599822998 s and adjustment time is 3.33987212181091 s ( 99.21 )
2024-12-19 23:13:57.003688 INFO::Formatting Data.
2024-12-19 23:13:57.004447 INFO::Replacing NaNs with NAs.
2024-12-19 23:13:57.005447 INFO::Removing potential empty rows and columns
2024-12-19 23:13:57.006493 INFO::Found 0 missing values.
2024-12-19 23:13:57.009795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:13:57.010493 INFO::Done
2024-12-19 23:13:57.011151 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:13:57.014072 INFO::Starting hierarchical adjustment
2024-12-19 23:13:57.015017 INFO::Found 5 batches.
2024-12-19 23:13:57.015695 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:13:57.016787 INFO::Using default BPPARAM
2024-12-19 23:13:57.017895 INFO::Processing subtree level 1
2024-12-19 23:14:00.324168 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:14:00.32554 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:14:00.338108 INFO::Done
2024-12-19 23:14:00.338974 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:00.341994 INFO::ASW Batch was 0.490309876582596 prior to batch effect correction and is now -0.0679424319383092 .
2024-12-19 23:14:00.342778 INFO::ASW Label was 0.342868028510102 prior to batch effect correction and is now 0.724373398562586 .
2024-12-19 23:14:00.343786 INFO::Total function execution time is 3.34007096290588 s and adjustment time is 3.32319307327271 s ( 99.49 )
2024-12-19 23:14:00.36423 INFO::Formatting Data.
2024-12-19 23:14:00.365753 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:00.367493 INFO::Removing potential empty rows and columns
2024-12-19 23:14:00.369272 INFO::Found 0 missing values.
2024-12-19 23:14:00.373307 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:00.374495 INFO::Done
2024-12-19 23:14:00.3757 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:00.380404 INFO::Starting hierarchical adjustment
2024-12-19 23:14:00.38184 INFO::Found 2 batches.
2024-12-19 23:14:00.383034 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:14:00.384237 INFO::Using default BPPARAM
2024-12-19 23:14:00.385385 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:14:00.38708 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:14:00.405671 INFO::Done
2024-12-19 23:14:00.407074 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:00.411682 INFO::ASW Batch was 0.568848668638415 prior to batch effect correction and is now -0.0250727336462848 .
2024-12-19 23:14:00.412996 INFO::ASW Label was 0.416380633794824 prior to batch effect correction and is now 0.825486016277166 .
2024-12-19 23:14:00.414512 INFO::Total function execution time is 0.0503909587860107 s and adjustment time is 0.0239949226379395 s ( 47.62 )
2024-12-19 23:14:00.415995 INFO::Formatting Data.
2024-12-19 23:14:00.417272 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:00.418878 INFO::Removing potential empty rows and columns
2024-12-19 23:14:00.420593 INFO::Found 0 missing values.
2024-12-19 23:14:00.42452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:00.4257 INFO::Done
2024-12-19 23:14:00.426851 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:00.43152 INFO::Starting hierarchical adjustment
2024-12-19 23:14:00.432928 INFO::Found 2 batches.
2024-12-19 23:14:00.434054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:14:00.435249 INFO::Using default BPPARAM
2024-12-19 23:14:00.436328 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:14:00.437946 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:14:00.456377 INFO::Done
2024-12-19 23:14:00.457711 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:00.462191 INFO::ASW Batch was 0.568848668638415 prior to batch effect correction and is now -0.0250727336462848 .
2024-12-19 23:14:00.463436 INFO::ASW Label was 0.416380633794824 prior to batch effect correction and is now 0.825486016277166 .
2024-12-19 23:14:00.464886 INFO::Total function execution time is 0.048893928527832 s and adjustment time is 0.0236489772796631 s ( 48.37 )
2024-12-19 23:14:00.483702 INFO::Formatting Data.
2024-12-19 23:14:00.485101 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:00.486678 INFO::Removing potential empty rows and columns
2024-12-19 23:14:00.488222 INFO::Found 0 missing values.
2024-12-19 23:14:00.491162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:00.492184 INFO::Done
2024-12-19 23:14:00.493249 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:00.496159 INFO::Starting hierarchical adjustment
2024-12-19 23:14:00.497412 INFO::Found 2 batches.
2024-12-19 23:14:00.498443 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:14:00.499587 INFO::Using default BPPARAM
2024-12-19 23:14:00.500603 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:14:00.502122 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:14:00.533483 INFO::Done
2024-12-19 23:14:00.534423 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:00.536605 INFO::ASW Batch was -0.00721118270360756 prior to batch effect correction and is now -0.0596408590682344 .
2024-12-19 23:14:00.53765 INFO::Total function execution time is 0.0541090965270996 s and adjustment time is 0.0362460613250732 s ( 66.99 )
2024-12-19 23:14:00.558953 INFO::Formatting Data.
2024-12-19 23:14:00.560588 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:00.562459 INFO::Removing potential empty rows and columns
2024-12-19 23:14:00.564415 INFO::Found 0 missing values.
2024-12-19 23:14:00.566544 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.
2024-12-19 23:14:00.573773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:00.575182 INFO::Done
2024-12-19 23:14:00.576512 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:00.58105 INFO::Starting hierarchical adjustment
2024-12-19 23:14:00.582499 INFO::Found 2 batches.
2024-12-19 23:14:00.583663 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:14:00.584889 INFO::Using default BPPARAM
2024-12-19 23:14:00.586004 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:14:00.587703 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:14:00.608396 INFO::Done
2024-12-19 23:14:00.609754 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:00.614389 INFO::ASW Batch was 0.610920395006919 prior to batch effect correction and is now -0.0185991790059097 .
2024-12-19 23:14:00.615717 INFO::ASW Label was 0.456181257167621 prior to batch effect correction and is now 0.903928166265395 .
2024-12-19 23:14:00.617188 INFO::Total function execution time is 0.0583860874176025 s and adjustment time is 0.0260720252990723 s ( 44.65 )
2024-12-19 23:14:00.618645 INFO::Formatting Data.
2024-12-19 23:14:00.619892 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:00.621548 INFO::Removing potential empty rows and columns
2024-12-19 23:14:00.623271 INFO::Found 0 missing values.
2024-12-19 23:14:00.624927 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.
2024-12-19 23:14:00.63153 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:00.632897 INFO::Done
2024-12-19 23:14:00.634178 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:00.639053 INFO::Starting hierarchical adjustment
2024-12-19 23:14:00.6406 INFO::Found 2 batches.
2024-12-19 23:14:00.641801 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:14:00.643125 INFO::Using default BPPARAM
2024-12-19 23:14:00.644295 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:14:00.64611 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:14:00.67111 INFO::Done
2024-12-19 23:14:00.672669 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:00.67827 INFO::ASW Batch was 0.610920395006919 prior to batch effect correction and is now -0.0185991790059097 .
2024-12-19 23:14:00.679769 INFO::ASW Label was 0.456181257167621 prior to batch effect correction and is now 0.903928166265395 .
2024-12-19 23:14:00.681556 INFO::Total function execution time is 0.0628509521484375 s and adjustment time is 0.030703067779541 s ( 48.85 )
2024-12-19 23:14:00.936183 INFO::Formatting Data.
2024-12-19 23:14:00.937264 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:00.93858 INFO::Removing potential empty rows and columns
2024-12-19 23:14:00.939939 INFO::Found 0 missing values.
2024-12-19 23:14:00.943366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:00.944163 INFO::Done
2024-12-19 23:14:00.944947 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:00.947381 INFO::Starting hierarchical adjustment
2024-12-19 23:14:00.948339 INFO::Found 3 batches.
2024-12-19 23:14:00.949196 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:14:00.950057 INFO::Using default BPPARAM
2024-12-19 23:14:00.950868 INFO::Processing subtree level 1
2024-12-19 23:14:03.741416 INFO::Adjusting the last 1 batches sequentially
2024-12-19 23:14:03.743748 INFO::Done
2024-12-19 23:14:03.74517 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:03.748723 INFO::ASW Batch was -0.111798129772201 prior to batch effect correction and is now -0.111798129772201 .
2024-12-19 23:14:03.750472 INFO::Total function execution time is 2.81431698799133 s and adjustment time is 2.79549503326416 s ( 99.33 )
2024-12-19 23:14:03.752459 INFO::Formatting Data.
2024-12-19 23:14:03.753908 INFO::Typecasting input to dataframe.
2024-12-19 23:14:03.755513 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:03.757329 INFO::Removing potential empty rows and columns
2024-12-19 23:14:03.759162 INFO::Found 0 missing values.
2024-12-19 23:14:03.76388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:03.765179 INFO::Done
2024-12-19 23:14:03.766367 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:03.769824 INFO::Starting hierarchical adjustment
2024-12-19 23:14:03.771276 INFO::Found 3 batches.
2024-12-19 23:14:03.772466 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:14:03.77378 INFO::Using default BPPARAM
2024-12-19 23:14:03.774936 INFO::Processing subtree level 1
2024-12-19 23:14:06.612363 INFO::Adjusting the last 1 batches sequentially
2024-12-19 23:14:06.613934 INFO::Done
2024-12-19 23:14:06.614821 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:06.617235 INFO::ASW Batch was -0.111798129772201 prior to batch effect correction and is now -0.111798129772201 .
2024-12-19 23:14:06.618261 INFO::Total function execution time is 2.86591696739197 s and adjustment time is 2.84290194511414 s ( 99.2 )
2024-12-19 23:14:06.633642 INFO::Formatting Data.
2024-12-19 23:14:06.634625 INFO::Typecasting input to dataframe.
2024-12-19 23:14:06.63565 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:06.636686 INFO::Removing potential empty rows and columns
2024-12-19 23:14:06.637854 INFO::Found 0 missing values.
2024-12-19 23:14:06.640502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:06.641215 INFO::Done
2024-12-19 23:14:06.641983 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:06.644214 INFO::Starting hierarchical adjustment
2024-12-19 23:14:06.64511 INFO::Found 3 batches.
2024-12-19 23:14:06.645947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:14:06.647131 INFO::Using default BPPARAM
2024-12-19 23:14:06.64818 INFO::Processing subtree level 1
2024-12-19 23:14:09.523755 INFO::Adjusting the last 1 batches sequentially
2024-12-19 23:14:09.526129 INFO::Done
2024-12-19 23:14:09.527464 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:09.5309 INFO::ASW Batch was -0.121451379540853 prior to batch effect correction and is now -0.121451379540853 .
2024-12-19 23:14:09.532476 INFO::Total function execution time is 2.89883899688721 s and adjustment time is 2.8810830116272 s ( 99.39 )
2024-12-19 23:14:12.516033 INFO::Formatting Data.
2024-12-19 23:14:12.517704 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:12.519845 INFO::Removing potential empty rows and columns
2024-12-19 23:14:12.523652 INFO::Found 1000 missing values.
2024-12-19 23:14:12.546859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:12.548331 INFO::Done
2024-12-19 23:14:12.549672 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:12.559679 INFO::Starting hierarchical adjustment
2024-12-19 23:14:12.561412 INFO::Found 10 batches.
2024-12-19 23:14:12.562707 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:14:12.564053 INFO::Using default BPPARAM
2024-12-19 23:14:12.565261 INFO::Processing subtree level 1
2024-12-19 23:14:15.766792 INFO::Processing subtree level 2
2024-12-19 23:14:18.813181 INFO::Adjusting the last 1 batches sequentially
2024-12-19 23:14:18.81576 INFO::Done
2024-12-19 23:14:18.817135 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:18.8269 INFO::ASW Batch was 0.457619231898296 prior to batch effect correction and is now 0.457619231898296 .
2024-12-19 23:14:18.828392 INFO::ASW Label was 0.366363167799204 prior to batch effect correction and is now 0.366363167799204 .
2024-12-19 23:14:18.830209 INFO::Total function execution time is 6.31427097320557 s and adjustment time is 6.2546329498291 s ( 99.06 )
2024-12-19 23:14:18.831867 INFO::Formatting Data.
2024-12-19 23:14:18.833219 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:18.835183 INFO::Removing potential empty rows and columns
2024-12-19 23:14:18.839005 INFO::Found 1000 missing values.
2024-12-19 23:14:18.860638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:18.861778 INFO::Done
2024-12-19 23:14:18.862618 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:18.872449 INFO::Starting hierarchical adjustment
2024-12-19 23:14:18.87413 INFO::Found 10 batches.
2024-12-19 23:14:19.666314 INFO::Set up parallel execution backend with 2 workers
2024-12-19 23:14:19.667757 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-12-19 23:14:22.874802 INFO::Adjusting the last 2 batches sequentially
2024-12-19 23:14:22.876855 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-19 23:14:22.89957 INFO::Done
2024-12-19 23:14:22.900906 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:22.910144 INFO::ASW Batch was 0.457619231898296 prior to batch effect correction and is now 0.457619231898296 .
2024-12-19 23:14:22.911454 INFO::ASW Label was 0.366363167799204 prior to batch effect correction and is now 0.366363167799204 .
2024-12-19 23:14:22.912902 INFO::Total function execution time is 4.08114385604858 s and adjustment time is 4.02568387985229 s ( 98.64 )
2024-12-19 23:14:25.695289 INFO::Formatting Data.
2024-12-19 23:14:25.696874 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:25.698642 INFO::Removing potential empty rows and columns
2024-12-19 23:14:25.700442 INFO::Found 0 missing values.
2024-12-19 23:14:25.70582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:25.707048 INFO::Done
2024-12-19 23:14:25.708228 INFO::Acquiring quality metrics before batch effect correction.
2024-12-19 23:14:25.712575 INFO::Starting hierarchical adjustment
2024-12-19 23:14:25.713956 INFO::Found 3 batches.
2024-12-19 23:14:25.715139 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-19 23:14:25.716398 INFO::Using default BPPARAM
2024-12-19 23:14:25.717488 INFO::Processing subtree level 1
2024-12-19 23:14:29.016641 INFO::Adjusting the last 1 batches sequentially
2024-12-19 23:14:29.019132 INFO::Done
2024-12-19 23:14:29.02059 INFO::Acquiring quality metrics after batch effect correction.
2024-12-19 23:14:29.025452 INFO::ASW Batch was 0.155592780524739 prior to batch effect correction and is now -0.110522335513367 .
2024-12-19 23:14:29.026939 INFO::ASW Label was -0.166845170140545 prior to batch effect correction and is now -0.0763595820259473 .
2024-12-19 23:14:29.028659 INFO::Total function execution time is 3.33343601226807 s and adjustment time is 3.30533003807068 s ( 99.16 )
2024-12-19 23:14:29.219375 INFO::Formatting Data.
2024-12-19 23:14:29.220816 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:29.222441 INFO::Removing potential empty rows and columns
2024-12-19 23:14:29.224136 INFO::Found 2 missing values.
2024-12-19 23:14:29.22821 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:29.229323 INFO::Done
2024-12-19 23:14:29.279446 INFO::Found NA in Reference column
2024-12-19 23:14:29.296815 INFO::Require at least two references per batch.
2024-12-19 23:14:29.3189 INFO::Formatting Data.
2024-12-19 23:14:29.319837 INFO::Recognized SummarizedExperiment
2024-12-19 23:14:29.320602 INFO::Typecasting input to dataframe.
2024-12-19 23:14:29.328757 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:29.330068 INFO::Removing potential empty rows and columns
2024-12-19 23:14:29.332812 INFO::Found 0 missing values.
2024-12-19 23:14:29.337954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:29.338792 INFO::Done
2024-12-19 23:14:29.353186 INFO::Formatting Data.
2024-12-19 23:14:29.354144 INFO::Recognized SummarizedExperiment
2024-12-19 23:14:29.354927 INFO::Typecasting input to dataframe.
2024-12-19 23:14:29.369946 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:29.371341 INFO::Removing potential empty rows and columns
2024-12-19 23:14:29.374182 INFO::Found 0 missing values.
2024-12-19 23:14:29.38221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:29.38306 INFO::Done
2024-12-19 23:14:29.39719 INFO::Formatting Data.
2024-12-19 23:14:29.398111 INFO::Recognized SummarizedExperiment
2024-12-19 23:14:29.39881 INFO::Typecasting input to dataframe.
2024-12-19 23:14:29.420597 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:29.422393 INFO::Removing potential empty rows and columns
2024-12-19 23:14:29.424297 INFO::Found 0 missing values.
2024-12-19 23:14:29.426022 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.
2024-12-19 23:14:29.432425 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:29.433966 INFO::Done
2024-12-19 23:14:29.453785 INFO::Formatting Data.
2024-12-19 23:14:29.45537 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:29.457143 INFO::Removing potential empty rows and columns
2024-12-19 23:14:29.45909 INFO::Found 0 missing values.
2024-12-19 23:14:29.463531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:29.46478 INFO::Done
2024-12-19 23:14:29.486422 INFO::Formatting Data.
2024-12-19 23:14:29.487978 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:29.489802 INFO::Removing potential empty rows and columns
2024-12-19 23:14:29.491776 INFO::Found 0 missing values.
2024-12-19 23:14:29.496315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:29.497554 INFO::Done
2024-12-19 23:14:29.552919 INFO::Formatting Data.
2024-12-19 23:14:29.55449 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:29.556559 INFO::Removing potential empty rows and columns
2024-12-19 23:14:29.558687 INFO::Found 1 missing values.
2024-12-19 23:14:29.56287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:29.564146 INFO::Done
2024-12-19 23:14:29.598573 INFO::Formatting Data.
2024-12-19 23:14:29.600101 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:29.601863 INFO::Removing potential empty rows and columns
2024-12-19 23:14:29.603546 INFO::Found 2 missing values.
2024-12-19 23:14:29.605171 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.
2024-12-19 23:14:29.608527 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:29.609645 INFO::Done
2024-12-19 23:14:29.626845 INFO::Formatting Data.
2024-12-19 23:14:29.627844 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:29.628937 INFO::Removing potential empty rows and columns
2024-12-19 23:14:29.630025 INFO::Found 2 missing values.
2024-12-19 23:14:29.631694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:29.632394 INFO::Done
2024-12-19 23:14:29.646226 INFO::Formatting Data.
2024-12-19 23:14:29.647244 INFO::Typecasting input to dataframe.
2024-12-19 23:14:29.648245 INFO::Replacing NaNs with NAs.
2024-12-19 23:14:29.649287 INFO::Removing potential empty rows and columns
2024-12-19 23:14:29.650398 INFO::Found 0 missing values.
2024-12-19 23:14:29.653121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-19 23:14:29.653861 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
31.48 1.70 79.35
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.94 | 0.69 | 18.63 | |
| compute_asw | 0.05 | 0.00 | 0.05 | |
| count_existing | 0.02 | 0.00 | 0.01 | |
| generate_data_covariables | 0.03 | 0.00 | 0.03 | |
| generate_dataset | 0.01 | 0.00 | 0.02 | |