Yannis Schumann
| Snapshot Date: 2025-02-05 13:48 -0500 (Wed, 05 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: f785e17 |
| git_last_commit_date: 2025-01-29 01:54:20 -0500 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-06 11:40 -0500 (Thu, 06 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4480 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4444 |
| 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 159/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.6 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 1.3.6 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.3.6.tar.gz |
| StartedAt: 2025-02-05 23:24:03 -0500 (Wed, 05 Feb 2025) |
| EndedAt: 2025-02-05 23:26:20 -0500 (Wed, 05 Feb 2025) |
| EllapsedTime: 137.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 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 '1.3.6'
* 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 9.5 0.46 19.18
* 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-3.21-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'BERT' ... ** this is package 'BERT' version '1.3.6' ** 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 Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 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")
2025-02-05 23:25:08.485767 INFO::Formatting Data.
2025-02-05 23:25:08.488471 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:08.501909 INFO::Removing potential empty rows and columns
2025-02-05 23:25:08.702422 INFO::Found 0 missing values.
2025-02-05 23:25:08.705401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:08.706222 INFO::Done
2025-02-05 23:25:08.706946 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:08.720119 INFO::Starting hierarchical adjustment
2025-02-05 23:25:08.721243 INFO::Found 3 batches.
2025-02-05 23:25:08.721982 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:08.723316 INFO::Using default BPPARAM
2025-02-05 23:25:08.724037 INFO::Processing subtree level 1
2025-02-05 23:25:11.25871 INFO::Adjusting the last 1 batches sequentially
2025-02-05 23:25:11.260582 INFO::Done
2025-02-05 23:25:11.261793 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:11.264056 INFO::ASW Batch was -0.0558514002352994 prior to batch effect correction and is now -0.0558514002352994 .
2025-02-05 23:25:11.265347 INFO::Total function execution time is 2.78024005889893 s and adjustment time is 2.53948521614075 s ( 91.34 )
2025-02-05 23:25:11.285846 INFO::Formatting Data.
2025-02-05 23:25:11.287544 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:11.289435 INFO::Removing potential empty rows and columns
2025-02-05 23:25:11.291453 INFO::Found 0 missing values.
2025-02-05 23:25:11.293388 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.
2025-02-05 23:25:11.306009 INFO::Formatting Data.
2025-02-05 23:25:11.307072 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:11.308232 INFO::Removing potential empty rows and columns
2025-02-05 23:25:11.309353 INFO::Found 0 missing values.
2025-02-05 23:25:11.310449 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.
2025-02-05 23:25:11.328084 INFO::Formatting Data.
2025-02-05 23:25:11.329043 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:11.330143 INFO::Removing potential empty rows and columns
2025-02-05 23:25:11.331316 INFO::Found 0 missing values.
2025-02-05 23:25:11.332401 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.
2025-02-05 23:25:11.336026 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:11.336772 INFO::Done
2025-02-05 23:25:11.337482 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:11.339504 INFO::Starting hierarchical adjustment
2025-02-05 23:25:11.340372 INFO::Found 2 batches.
2025-02-05 23:25:11.341158 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:11.341949 INFO::Using default BPPARAM
2025-02-05 23:25:11.342644 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:11.343706 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:11.359912 INFO::Done
2025-02-05 23:25:11.360838 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:11.362983 INFO::ASW Batch was 0.0963118670466038 prior to batch effect correction and is now -0.115058024383331 .
2025-02-05 23:25:11.363958 INFO::Total function execution time is 0.0359318256378174 s and adjustment time is 0.0196399688720703 s ( 54.66 )
2025-02-05 23:25:11.366825 INFO::Formatting Data.
2025-02-05 23:25:11.367666 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:11.374872 INFO::Formatting Data.
2025-02-05 23:25:11.375732 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:11.376723 INFO::Removing potential empty rows and columns
2025-02-05 23:25:11.377937 INFO::Found 0 missing values.
2025-02-05 23:25:11.380622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:11.381413 INFO::Done
2025-02-05 23:25:11.382189 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:11.384346 INFO::Starting hierarchical adjustment
2025-02-05 23:25:11.385259 INFO::Found 2 batches.
2025-02-05 23:25:11.386045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:11.386839 INFO::Using default BPPARAM
2025-02-05 23:25:11.387622 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:11.388718 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:11.40293 INFO::Done
2025-02-05 23:25:11.404252 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:11.407404 INFO::ASW Batch was 0.0191605220462131 prior to batch effect correction and is now -0.123430731969606 .
2025-02-05 23:25:11.40882 INFO::Total function execution time is 0.033937931060791 s and adjustment time is 0.0177459716796875 s ( 52.29 )
2025-02-05 23:25:11.410633 INFO::Formatting Data.
2025-02-05 23:25:11.411856 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:11.413457 INFO::Removing potential empty rows and columns
2025-02-05 23:25:11.415238 INFO::Found 0 missing values.
2025-02-05 23:25:11.419397 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:11.420505 INFO::Done
2025-02-05 23:25:11.421624 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:11.424785 INFO::Starting hierarchical adjustment
2025-02-05 23:25:11.426152 INFO::Found 2 batches.
2025-02-05 23:25:11.427266 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:11.428543 INFO::Using default BPPARAM
2025-02-05 23:25:11.429667 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:11.431269 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:11.451326 INFO::Done
2025-02-05 23:25:11.45266 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:11.455913 INFO::ASW Batch was 0.0191605220462131 prior to batch effect correction and is now -0.123430731969606 .
2025-02-05 23:25:11.4574 INFO::Total function execution time is 0.0467329025268555 s and adjustment time is 0.0253410339355469 s ( 54.23 )
2025-02-05 23:25:13.992439 INFO::Formatting Data.
2025-02-05 23:25:13.993395 INFO::Recognized SummarizedExperiment
2025-02-05 23:25:13.99414 INFO::Typecasting input to dataframe.
2025-02-05 23:25:14.217262 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:14.218613 INFO::Removing potential empty rows and columns
2025-02-05 23:25:14.221464 INFO::Found 0 missing values.
2025-02-05 23:25:14.226877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:14.227765 INFO::Done
2025-02-05 23:25:14.228504 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:14.23212 INFO::Starting hierarchical adjustment
2025-02-05 23:25:14.233023 INFO::Found 2 batches.
2025-02-05 23:25:14.233717 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:14.234961 INFO::Using default BPPARAM
2025-02-05 23:25:14.235672 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:14.236835 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:14.278784 INFO::Done
2025-02-05 23:25:14.279638 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:14.283142 INFO::ASW Batch was 0.00710953418696005 prior to batch effect correction and is now -0.0847240710034693 .
2025-02-05 23:25:14.28419 INFO::Total function execution time is 0.292053937911987 s and adjustment time is 0.0458710193634033 s ( 15.71 )
2025-02-05 23:25:14.301921 INFO::Formatting Data.
2025-02-05 23:25:14.302859 INFO::Recognized SummarizedExperiment
2025-02-05 23:25:14.303601 INFO::Typecasting input to dataframe.
2025-02-05 23:25:14.311326 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:14.312632 INFO::Removing potential empty rows and columns
2025-02-05 23:25:14.315569 INFO::Found 0 missing values.
2025-02-05 23:25:14.320855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:14.321647 INFO::Done
2025-02-05 23:25:14.322356 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:14.325967 INFO::Starting hierarchical adjustment
2025-02-05 23:25:14.326937 INFO::Found 2 batches.
2025-02-05 23:25:14.327745 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:14.328569 INFO::Using default BPPARAM
2025-02-05 23:25:14.329299 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:14.330456 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:15.028043 INFO::Done
2025-02-05 23:25:15.029404 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:15.034923 INFO::ASW Batch was -0.000596781573979903 prior to batch effect correction and is now -0.000596781573979903 .
2025-02-05 23:25:15.036481 INFO::Total function execution time is 0.734473943710327 s and adjustment time is 0.701149940490723 s ( 95.46 )
2025-02-05 23:25:15.066571 INFO::Formatting Data.
2025-02-05 23:25:15.068051 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:15.069726 INFO::Removing potential empty rows and columns
2025-02-05 23:25:15.071511 INFO::Found 0 missing values.
2025-02-05 23:25:15.075747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:15.076927 INFO::Done
2025-02-05 23:25:15.07805 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:15.081162 INFO::Starting hierarchical adjustment
2025-02-05 23:25:15.082502 INFO::Found 3 batches.
2025-02-05 23:25:15.083597 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:15.084788 INFO::Using default BPPARAM
2025-02-05 23:25:15.085861 INFO::Processing subtree level 1
2025-02-05 23:25:25.266661 INFO::Adjusting the last 1 batches sequentially
2025-02-05 23:25:25.26893 INFO::Done
2025-02-05 23:25:25.270228 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:25.273683 INFO::ASW Batch was -0.08346060488496 prior to batch effect correction and is now -0.157942617216814 .
2025-02-05 23:25:25.275276 INFO::Total function execution time is 10.208832025528 s and adjustment time is 10.1866068840027 s ( 99.78 )
2025-02-05 23:25:25.300595 INFO::Skipping initial DF formatting
2025-02-05 23:25:25.302012 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:25.308765 INFO::Starting hierarchical adjustment
2025-02-05 23:25:25.310467 INFO::Found 5 batches.
2025-02-05 23:25:25.311786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:25.313142 INFO::Using default BPPARAM
2025-02-05 23:25:25.314406 INFO::Processing subtree level 1
2025-02-05 23:25:28.587968 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:28.590138 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:28.606748 INFO::Done
2025-02-05 23:25:28.6079 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:28.614463 INFO::ASW Batch was 0.487801409299328 prior to batch effect correction and is now 0.487801409299328 .
2025-02-05 23:25:28.61588 INFO::ASW Label was 0.413138046211872 prior to batch effect correction and is now 0.413138046211872 .
2025-02-05 23:25:28.617644 INFO::Total function execution time is 3.31712293624878 s and adjustment time is 3.29655504226685 s ( 99.38 )
2025-02-05 23:25:28.647527 INFO::Formatting Data.
2025-02-05 23:25:28.649297 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:28.651277 INFO::Removing potential empty rows and columns
2025-02-05 23:25:28.653175 INFO::Found 0 missing values.
2025-02-05 23:25:28.659103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:28.66052 INFO::Done
2025-02-05 23:25:28.661854 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:28.666834 INFO::Starting hierarchical adjustment
2025-02-05 23:25:28.668357 INFO::Found 5 batches.
2025-02-05 23:25:28.669573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:28.670943 INFO::Using default BPPARAM
2025-02-05 23:25:28.672176 INFO::Processing subtree level 1
2025-02-05 23:25:31.881839 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:31.88378 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:31.90171 INFO::Done
2025-02-05 23:25:31.902979 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:31.907609 INFO::ASW Batch was 0.293574010517072 prior to batch effect correction and is now -0.0833558779852916 .
2025-02-05 23:25:31.908926 INFO::ASW Label was 0.388056684518527 prior to batch effect correction and is now 0.888551329926954 .
2025-02-05 23:25:31.91039 INFO::Total function execution time is 3.26300716400146 s and adjustment time is 3.23354196548462 s ( 99.1 )
2025-02-05 23:25:31.911828 INFO::Formatting Data.
2025-02-05 23:25:31.913072 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:31.914606 INFO::Removing potential empty rows and columns
2025-02-05 23:25:31.916226 INFO::Found 0 missing values.
2025-02-05 23:25:31.921066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:31.922087 INFO::Done
2025-02-05 23:25:31.923092 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:31.927261 INFO::Starting hierarchical adjustment
2025-02-05 23:25:31.928532 INFO::Found 5 batches.
2025-02-05 23:25:31.929243 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:31.929985 INFO::Using default BPPARAM
2025-02-05 23:25:31.930654 INFO::Processing subtree level 1
2025-02-05 23:25:35.122571 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:35.124385 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:35.14358 INFO::Done
2025-02-05 23:25:35.144888 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:35.14971 INFO::ASW Batch was 0.293574010517072 prior to batch effect correction and is now -0.0833558779852916 .
2025-02-05 23:25:35.151027 INFO::ASW Label was 0.388056684518527 prior to batch effect correction and is now 0.888551329926954 .
2025-02-05 23:25:35.152583 INFO::Total function execution time is 3.24076199531555 s and adjustment time is 3.21518301963806 s ( 99.21 )
2025-02-05 23:25:35.174264 INFO::Formatting Data.
2025-02-05 23:25:35.175706 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:35.177311 INFO::Removing potential empty rows and columns
2025-02-05 23:25:35.178958 INFO::Found 0 missing values.
2025-02-05 23:25:35.18401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:35.185204 INFO::Done
2025-02-05 23:25:35.186334 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:35.190693 INFO::Starting hierarchical adjustment
2025-02-05 23:25:35.192129 INFO::Found 5 batches.
2025-02-05 23:25:35.193267 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:35.19448 INFO::Using default BPPARAM
2025-02-05 23:25:35.195593 INFO::Processing subtree level 1
2025-02-05 23:25:38.343328 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:38.34545 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:38.364442 INFO::Done
2025-02-05 23:25:38.365929 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:38.370771 INFO::ASW Batch was 0.257894113201612 prior to batch effect correction and is now -0.0329532575363117 .
2025-02-05 23:25:38.372022 INFO::ASW Label was 0.401598552868823 prior to batch effect correction and is now 0.755067084318289 .
2025-02-05 23:25:38.373499 INFO::Total function execution time is 3.19933605194092 s and adjustment time is 3.17246389389038 s ( 99.16 )
2025-02-05 23:25:38.374997 INFO::Formatting Data.
2025-02-05 23:25:38.376234 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:38.377776 INFO::Removing potential empty rows and columns
2025-02-05 23:25:38.379402 INFO::Found 0 missing values.
2025-02-05 23:25:38.385281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:38.38661 INFO::Done
2025-02-05 23:25:38.3879 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:38.392636 INFO::Starting hierarchical adjustment
2025-02-05 23:25:38.394164 INFO::Found 5 batches.
2025-02-05 23:25:38.395426 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:38.396781 INFO::Using default BPPARAM
2025-02-05 23:25:38.398014 INFO::Processing subtree level 1
2025-02-05 23:25:41.783065 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:41.784785 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:41.803583 INFO::Done
2025-02-05 23:25:41.804915 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:41.809402 INFO::ASW Batch was 0.257894113201612 prior to batch effect correction and is now -0.0329532575363117 .
2025-02-05 23:25:41.810603 INFO::ASW Label was 0.401598552868823 prior to batch effect correction and is now 0.755067084318289 .
2025-02-05 23:25:41.812029 INFO::Total function execution time is 3.43705892562866 s and adjustment time is 3.40959811210632 s ( 99.2 )
2025-02-05 23:25:41.835266 INFO::Formatting Data.
2025-02-05 23:25:41.836769 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:41.838475 INFO::Removing potential empty rows and columns
2025-02-05 23:25:41.840248 INFO::Found 0 missing values.
2025-02-05 23:25:41.844161 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:41.845355 INFO::Done
2025-02-05 23:25:41.846508 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:41.85099 INFO::Starting hierarchical adjustment
2025-02-05 23:25:41.852435 INFO::Found 2 batches.
2025-02-05 23:25:41.853605 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:41.854874 INFO::Using default BPPARAM
2025-02-05 23:25:41.856036 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:41.857707 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:41.876706 INFO::Done
2025-02-05 23:25:41.878175 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:41.882896 INFO::ASW Batch was 0.307314240085457 prior to batch effect correction and is now 0.16414739617681 .
2025-02-05 23:25:41.884135 INFO::ASW Label was 0.784330520174749 prior to batch effect correction and is now 0.822166223406688 .
2025-02-05 23:25:41.885691 INFO::Total function execution time is 0.0505149364471436 s and adjustment time is 0.0244438648223877 s ( 48.39 )
2025-02-05 23:25:41.887204 INFO::Formatting Data.
2025-02-05 23:25:41.888509 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:41.890144 INFO::Removing potential empty rows and columns
2025-02-05 23:25:41.891951 INFO::Found 0 missing values.
2025-02-05 23:25:41.895774 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:41.896885 INFO::Done
2025-02-05 23:25:41.898051 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:41.902698 INFO::Starting hierarchical adjustment
2025-02-05 23:25:41.904164 INFO::Found 2 batches.
2025-02-05 23:25:41.905338 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:41.906651 INFO::Using default BPPARAM
2025-02-05 23:25:41.907846 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:41.909528 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:41.928728 INFO::Done
2025-02-05 23:25:41.930126 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:41.934874 INFO::ASW Batch was 0.307314240085457 prior to batch effect correction and is now 0.16414739617681 .
2025-02-05 23:25:41.936192 INFO::ASW Label was 0.784330520174749 prior to batch effect correction and is now 0.822166223406688 .
2025-02-05 23:25:41.937771 INFO::Total function execution time is 0.0505480766296387 s and adjustment time is 0.0247330665588379 s ( 48.93 )
2025-02-05 23:25:41.960593 INFO::Formatting Data.
2025-02-05 23:25:41.962141 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:41.963867 INFO::Removing potential empty rows and columns
2025-02-05 23:25:41.965592 INFO::Found 0 missing values.
2025-02-05 23:25:41.969058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:41.970323 INFO::Done
2025-02-05 23:25:41.971532 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:41.974737 INFO::Starting hierarchical adjustment
2025-02-05 23:25:41.976202 INFO::Found 2 batches.
2025-02-05 23:25:41.977434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:41.978724 INFO::Using default BPPARAM
2025-02-05 23:25:41.979993 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:41.981806 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:42.023068 INFO::Done
2025-02-05 23:25:42.024496 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:42.027729 INFO::ASW Batch was 0.18613766808952 prior to batch effect correction and is now -0.136282032050991 .
2025-02-05 23:25:42.029337 INFO::Total function execution time is 0.068850040435791 s and adjustment time is 0.0470409393310547 s ( 68.32 )
2025-02-05 23:25:42.0531 INFO::Formatting Data.
2025-02-05 23:25:42.054627 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:42.056388 INFO::Removing potential empty rows and columns
2025-02-05 23:25:42.058307 INFO::Found 0 missing values.
2025-02-05 23:25:42.060369 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.
2025-02-05 23:25:42.067283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:42.068721 INFO::Done
2025-02-05 23:25:42.07004 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:42.07487 INFO::Starting hierarchical adjustment
2025-02-05 23:25:42.076499 INFO::Found 2 batches.
2025-02-05 23:25:42.07778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:42.079118 INFO::Using default BPPARAM
2025-02-05 23:25:42.080423 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:42.082307 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:42.10555 INFO::Done
2025-02-05 23:25:42.106985 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:42.11194 INFO::ASW Batch was 0.773657061184962 prior to batch effect correction and is now 0.0904248728727455 .
2025-02-05 23:25:42.113284 INFO::ASW Label was 0.29544552315324 prior to batch effect correction and is now 0.826220112188311 .
2025-02-05 23:25:42.114903 INFO::Total function execution time is 0.0619001388549805 s and adjustment time is 0.0292510986328125 s ( 47.26 )
2025-02-05 23:25:42.116466 INFO::Formatting Data.
2025-02-05 23:25:42.117804 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:42.119573 INFO::Removing potential empty rows and columns
2025-02-05 23:25:42.121463 INFO::Found 0 missing values.
2025-02-05 23:25:42.123217 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.
2025-02-05 23:25:42.130272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:42.131659 INFO::Done
2025-02-05 23:25:42.132931 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:42.137962 INFO::Starting hierarchical adjustment
2025-02-05 23:25:42.139586 INFO::Found 2 batches.
2025-02-05 23:25:42.140928 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:42.142299 INFO::Using default BPPARAM
2025-02-05 23:25:42.143556 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:25:42.145424 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:25:42.168987 INFO::Done
2025-02-05 23:25:42.170462 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:42.175458 INFO::ASW Batch was 0.773657061184962 prior to batch effect correction and is now 0.0904248728727455 .
2025-02-05 23:25:42.176847 INFO::ASW Label was 0.29544552315324 prior to batch effect correction and is now 0.826220112188311 .
2025-02-05 23:25:42.178515 INFO::Total function execution time is 0.0620460510253906 s and adjustment time is 0.0296089649200439 s ( 47.72 )
2025-02-05 23:25:42.484503 INFO::Formatting Data.
2025-02-05 23:25:42.485581 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:42.486853 INFO::Removing potential empty rows and columns
2025-02-05 23:25:42.48815 INFO::Found 0 missing values.
2025-02-05 23:25:42.491318 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:42.492103 INFO::Done
2025-02-05 23:25:42.492909 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:42.495279 INFO::Starting hierarchical adjustment
2025-02-05 23:25:42.496266 INFO::Found 3 batches.
2025-02-05 23:25:42.497044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:42.497918 INFO::Using default BPPARAM
2025-02-05 23:25:42.49869 INFO::Processing subtree level 1
2025-02-05 23:25:45.279574 INFO::Adjusting the last 1 batches sequentially
2025-02-05 23:25:45.281699 INFO::Done
2025-02-05 23:25:45.282998 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:45.286085 INFO::ASW Batch was -0.0543982677718191 prior to batch effect correction and is now -0.0543982677718191 .
2025-02-05 23:25:45.287601 INFO::Total function execution time is 2.80311918258667 s and adjustment time is 2.78554391860962 s ( 99.37 )
2025-02-05 23:25:45.289349 INFO::Formatting Data.
2025-02-05 23:25:45.290788 INFO::Typecasting input to dataframe.
2025-02-05 23:25:45.292291 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:45.293838 INFO::Removing potential empty rows and columns
2025-02-05 23:25:45.295472 INFO::Found 0 missing values.
2025-02-05 23:25:45.299421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:45.300544 INFO::Done
2025-02-05 23:25:45.301646 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:45.304654 INFO::Starting hierarchical adjustment
2025-02-05 23:25:45.305938 INFO::Found 3 batches.
2025-02-05 23:25:45.307124 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:45.308381 INFO::Using default BPPARAM
2025-02-05 23:25:45.309583 INFO::Processing subtree level 1
2025-02-05 23:25:48.335243 INFO::Adjusting the last 1 batches sequentially
2025-02-05 23:25:48.337563 INFO::Done
2025-02-05 23:25:48.338906 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:48.342193 INFO::ASW Batch was -0.0543982677718191 prior to batch effect correction and is now -0.0543982677718191 .
2025-02-05 23:25:48.343794 INFO::Total function execution time is 3.05445694923401 s and adjustment time is 3.03179216384888 s ( 99.26 )
2025-02-05 23:25:48.364611 INFO::Formatting Data.
2025-02-05 23:25:48.365936 INFO::Typecasting input to dataframe.
2025-02-05 23:25:48.367659 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:48.369255 INFO::Removing potential empty rows and columns
2025-02-05 23:25:48.370632 INFO::Found 0 missing values.
2025-02-05 23:25:48.373767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:48.374624 INFO::Done
2025-02-05 23:25:48.375417 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:48.377614 INFO::Starting hierarchical adjustment
2025-02-05 23:25:48.378593 INFO::Found 3 batches.
2025-02-05 23:25:48.379366 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:48.380244 INFO::Using default BPPARAM
2025-02-05 23:25:48.380994 INFO::Processing subtree level 1
2025-02-05 23:25:51.260068 INFO::Adjusting the last 1 batches sequentially
2025-02-05 23:25:51.262262 INFO::Done
2025-02-05 23:25:51.263451 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:25:51.266468 INFO::ASW Batch was -0.0997122686721225 prior to batch effect correction and is now -0.0997122686721225 .
2025-02-05 23:25:51.267882 INFO::Total function execution time is 2.90343403816223 s and adjustment time is 2.88375687599182 s ( 99.32 )
2025-02-05 23:25:54.33726 INFO::Formatting Data.
2025-02-05 23:25:54.338256 INFO::Replacing NaNs with NAs.
2025-02-05 23:25:54.339513 INFO::Removing potential empty rows and columns
2025-02-05 23:25:54.341737 INFO::Found 1000 missing values.
2025-02-05 23:25:54.35494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:25:54.355858 INFO::Done
2025-02-05 23:25:54.356663 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:25:54.362922 INFO::Starting hierarchical adjustment
2025-02-05 23:25:54.36418 INFO::Found 10 batches.
2025-02-05 23:25:54.364945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:25:54.365723 INFO::Using default BPPARAM
2025-02-05 23:25:54.36645 INFO::Processing subtree level 1
2025-02-05 23:25:57.490162 INFO::Processing subtree level 2
2025-02-05 23:26:00.380621 INFO::Adjusting the last 1 batches sequentially
2025-02-05 23:26:00.383253 INFO::Done
2025-02-05 23:26:00.384651 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:26:00.394001 INFO::ASW Batch was 0.469656176854776 prior to batch effect correction and is now 0.469656176854776 .
2025-02-05 23:26:00.395022 INFO::ASW Label was 0.338356159458156 prior to batch effect correction and is now 0.338356159458156 .
2025-02-05 23:26:00.396368 INFO::Total function execution time is 6.05918288230896 s and adjustment time is 6.01922202110291 s ( 99.34 )
2025-02-05 23:26:00.397528 INFO::Formatting Data.
2025-02-05 23:26:00.398494 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:00.400004 INFO::Removing potential empty rows and columns
2025-02-05 23:26:00.402392 INFO::Found 1000 missing values.
2025-02-05 23:26:00.41966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:00.421043 INFO::Done
2025-02-05 23:26:00.422279 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:26:00.431841 INFO::Starting hierarchical adjustment
2025-02-05 23:26:00.433481 INFO::Found 10 batches.
2025-02-05 23:26:01.189383 INFO::Set up parallel execution backend with 2 workers
2025-02-05 23:26:01.190912 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-05 23:26:03.981783 INFO::Adjusting the last 2 batches sequentially
2025-02-05 23:26:03.983912 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-05 23:26:04.006599 INFO::Done
2025-02-05 23:26:04.007853 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:26:04.016172 INFO::ASW Batch was 0.469656176854776 prior to batch effect correction and is now 0.469656176854776 .
2025-02-05 23:26:04.017415 INFO::ASW Label was 0.338356159458156 prior to batch effect correction and is now 0.338356159458156 .
2025-02-05 23:26:04.018824 INFO::Total function execution time is 3.62126803398132 s and adjustment time is 3.57337808609009 s ( 98.68 )
2025-02-05 23:26:06.956524 INFO::Formatting Data.
2025-02-05 23:26:06.957518 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:06.958605 INFO::Removing potential empty rows and columns
2025-02-05 23:26:06.959753 INFO::Found 0 missing values.
2025-02-05 23:26:06.962917 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:06.96365 INFO::Done
2025-02-05 23:26:06.964341 INFO::Acquiring quality metrics before batch effect correction.
2025-02-05 23:26:06.967082 INFO::Starting hierarchical adjustment
2025-02-05 23:26:06.967954 INFO::Found 3 batches.
2025-02-05 23:26:06.96865 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-05 23:26:06.969425 INFO::Using default BPPARAM
2025-02-05 23:26:06.970121 INFO::Processing subtree level 1
2025-02-05 23:26:09.878236 INFO::Adjusting the last 1 batches sequentially
2025-02-05 23:26:09.880285 INFO::Done
2025-02-05 23:26:09.881472 INFO::Acquiring quality metrics after batch effect correction.
2025-02-05 23:26:09.885324 INFO::ASW Batch was 0.172433238842395 prior to batch effect correction and is now -0.154529593895006 .
2025-02-05 23:26:09.886445 INFO::ASW Label was -0.190398465605977 prior to batch effect correction and is now -0.043012519269562 .
2025-02-05 23:26:09.887797 INFO::Total function execution time is 2.93132996559143 s and adjustment time is 2.91241598129272 s ( 99.35 )
2025-02-05 23:26:10.069599 INFO::Formatting Data.
2025-02-05 23:26:10.070564 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:10.071664 INFO::Removing potential empty rows and columns
2025-02-05 23:26:10.072746 INFO::Found 2 missing values.
2025-02-05 23:26:10.07516 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:10.075865 INFO::Done
2025-02-05 23:26:10.112734 INFO::Found NA in Reference column
2025-02-05 23:26:10.125558 INFO::Require at least two references per batch.
2025-02-05 23:26:10.145701 INFO::Formatting Data.
2025-02-05 23:26:10.146609 INFO::Recognized SummarizedExperiment
2025-02-05 23:26:10.147326 INFO::Typecasting input to dataframe.
2025-02-05 23:26:10.155153 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:10.156637 INFO::Removing potential empty rows and columns
2025-02-05 23:26:10.159301 INFO::Found 0 missing values.
2025-02-05 23:26:10.164251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:10.164998 INFO::Done
2025-02-05 23:26:10.178458 INFO::Formatting Data.
2025-02-05 23:26:10.179352 INFO::Recognized SummarizedExperiment
2025-02-05 23:26:10.180058 INFO::Typecasting input to dataframe.
2025-02-05 23:26:10.198421 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:10.20049 INFO::Removing potential empty rows and columns
2025-02-05 23:26:10.205089 INFO::Found 0 missing values.
2025-02-05 23:26:10.215483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:10.216469 INFO::Done
2025-02-05 23:26:10.231943 INFO::Formatting Data.
2025-02-05 23:26:10.232956 INFO::Recognized SummarizedExperiment
2025-02-05 23:26:10.233666 INFO::Typecasting input to dataframe.
2025-02-05 23:26:10.251347 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:10.252513 INFO::Removing potential empty rows and columns
2025-02-05 23:26:10.253751 INFO::Found 0 missing values.
2025-02-05 23:26:10.255049 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.
2025-02-05 23:26:10.258621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:10.25933 INFO::Done
2025-02-05 23:26:10.272871 INFO::Formatting Data.
2025-02-05 23:26:10.273864 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:10.274972 INFO::Removing potential empty rows and columns
2025-02-05 23:26:10.276131 INFO::Found 0 missing values.
2025-02-05 23:26:10.278754 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:10.279525 INFO::Done
2025-02-05 23:26:10.294427 INFO::Formatting Data.
2025-02-05 23:26:10.295409 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:10.29643 INFO::Removing potential empty rows and columns
2025-02-05 23:26:10.297538 INFO::Found 0 missing values.
2025-02-05 23:26:10.300082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:10.300837 INFO::Done
2025-02-05 23:26:10.339594 INFO::Formatting Data.
2025-02-05 23:26:10.340571 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:10.341721 INFO::Removing potential empty rows and columns
2025-02-05 23:26:10.342914 INFO::Found 1 missing values.
2025-02-05 23:26:10.345198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:10.345918 INFO::Done
2025-02-05 23:26:10.371346 INFO::Formatting Data.
2025-02-05 23:26:10.372357 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:10.373461 INFO::Removing potential empty rows and columns
2025-02-05 23:26:10.374601 INFO::Found 2 missing values.
2025-02-05 23:26:10.375695 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.
2025-02-05 23:26:10.377846 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:10.378614 INFO::Done
2025-02-05 23:26:10.39255 INFO::Formatting Data.
2025-02-05 23:26:10.393576 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:10.394671 INFO::Removing potential empty rows and columns
2025-02-05 23:26:10.395706 INFO::Found 2 missing values.
2025-02-05 23:26:10.397362 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:10.398101 INFO::Done
2025-02-05 23:26:10.412179 INFO::Formatting Data.
2025-02-05 23:26:10.41318 INFO::Typecasting input to dataframe.
2025-02-05 23:26:10.414187 INFO::Replacing NaNs with NAs.
2025-02-05 23:26:10.415241 INFO::Removing potential empty rows and columns
2025-02-05 23:26:10.416324 INFO::Found 0 missing values.
2025-02-05 23:26:10.418823 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-05 23:26:10.41953 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
30.68 1.60 77.53
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.50 | 0.46 | 19.18 | |
| compute_asw | 0.01 | 0.00 | 0.01 | |
| count_existing | 0.01 | 0.00 | 0.01 | |
| generate_data_covariables | 0.02 | 0.00 | 0.02 | |
| generate_dataset | 0.01 | 0.00 | 0.01 | |