Yannis Schumann
| Snapshot Date: 2025-03-23 13:40 -0400 (Sun, 23 Mar 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 -0400 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-24 11:40 -0400 (Mon, 24 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4779 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4550 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4530 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4461 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 161/2313 | 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 | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.3.6 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.6.tar.gz |
| StartedAt: 2025-03-23 20:13:03 -0400 (Sun, 23 Mar 2025) |
| EndedAt: 2025-03-23 20:14:33 -0400 (Sun, 23 Mar 2025) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 25.061 1.306 17.918
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2025-03-13 r87965) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-03-23 20:13:55.173159 INFO::Formatting Data.
2025-03-23 20:13:55.174855 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:55.186924 INFO::Removing potential empty rows and columns
2025-03-23 20:13:55.440446 INFO::Found 0 missing values.
2025-03-23 20:13:55.44415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:13:55.444913 INFO::Done
2025-03-23 20:13:55.445483 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:13:55.458058 INFO::Starting hierarchical adjustment
2025-03-23 20:13:55.459089 INFO::Found 3 batches.
2025-03-23 20:13:55.459673 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:13:55.461007 INFO::Using default BPPARAM
2025-03-23 20:13:55.461566 INFO::Processing subtree level 1
2025-03-23 20:13:55.566109 INFO::Adjusting the last 1 batches sequentially
2025-03-23 20:13:55.568078 INFO::Done
2025-03-23 20:13:55.568758 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:13:55.571877 INFO::ASW Batch was 0.00346704908738525 prior to batch effect correction and is now 0.00346704908738525 .
2025-03-23 20:13:55.573099 INFO::Total function execution time is 0.400735139846802 s and adjustment time is 0.109200716018677 s ( 27.25 )
2025-03-23 20:13:55.587902 INFO::Formatting Data.
2025-03-23 20:13:55.588708 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:55.589678 INFO::Removing potential empty rows and columns
2025-03-23 20:13:55.590793 INFO::Found 0 missing values.
2025-03-23 20:13:55.5918 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.
2025-03-23 20:13:55.603436 INFO::Formatting Data.
2025-03-23 20:13:55.604215 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:55.605161 INFO::Removing potential empty rows and columns
2025-03-23 20:13:55.606258 INFO::Found 0 missing values.
2025-03-23 20:13:55.607239 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.
2025-03-23 20:13:55.623916 INFO::Formatting Data.
2025-03-23 20:13:55.624729 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:55.625675 INFO::Removing potential empty rows and columns
2025-03-23 20:13:55.62677 INFO::Found 0 missing values.
2025-03-23 20:13:55.627793 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.
2025-03-23 20:13:55.63248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:13:55.633122 INFO::Done
2025-03-23 20:13:55.633677 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:13:55.635747 INFO::Starting hierarchical adjustment
2025-03-23 20:13:55.636463 INFO::Found 2 batches.
2025-03-23 20:13:55.637048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:13:55.6377 INFO::Using default BPPARAM
2025-03-23 20:13:55.63828 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:13:55.639264 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:13:55.66346 INFO::Done
2025-03-23 20:13:55.664204 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:13:55.666347 INFO::ASW Batch was 0.0742362119298376 prior to batch effect correction and is now -0.115812124260725 .
2025-03-23 20:13:55.667182 INFO::Total function execution time is 0.0433685779571533 s and adjustment time is 0.0271072387695312 s ( 62.5 )
2025-03-23 20:13:55.670094 INFO::Formatting Data.
2025-03-23 20:13:55.670725 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:55.68014 INFO::Formatting Data.
2025-03-23 20:13:55.681024 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:55.681997 INFO::Removing potential empty rows and columns
2025-03-23 20:13:55.683098 INFO::Found 0 missing values.
2025-03-23 20:13:55.686166 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:13:55.686734 INFO::Done
2025-03-23 20:13:55.687298 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:13:55.689589 INFO::Starting hierarchical adjustment
2025-03-23 20:13:55.690352 INFO::Found 2 batches.
2025-03-23 20:13:55.690956 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:13:55.69171 INFO::Using default BPPARAM
2025-03-23 20:13:55.692389 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:13:55.693575 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:13:55.723682 INFO::Done
2025-03-23 20:13:55.724773 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:13:55.727714 INFO::ASW Batch was -0.0886909941913449 prior to batch effect correction and is now -0.116243977890104 .
2025-03-23 20:13:55.728676 INFO::Total function execution time is 0.0485031604766846 s and adjustment time is 0.033393383026123 s ( 68.85 )
2025-03-23 20:13:55.730247 INFO::Formatting Data.
2025-03-23 20:13:55.730952 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:55.732028 INFO::Removing potential empty rows and columns
2025-03-23 20:13:55.733356 INFO::Found 0 missing values.
2025-03-23 20:13:55.736501 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:13:55.737088 INFO::Done
2025-03-23 20:13:55.737652 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:13:55.739915 INFO::Starting hierarchical adjustment
2025-03-23 20:13:55.740682 INFO::Found 2 batches.
2025-03-23 20:13:55.74126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:13:55.742033 INFO::Using default BPPARAM
2025-03-23 20:13:55.742769 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:13:55.743789 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:13:55.760083 INFO::Done
2025-03-23 20:13:55.760797 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:13:55.76311 INFO::ASW Batch was -0.0886909941913449 prior to batch effect correction and is now -0.116243977890104 .
2025-03-23 20:13:55.763955 INFO::Total function execution time is 0.0337300300598145 s and adjustment time is 0.0195374488830566 s ( 57.92 )
2025-03-23 20:13:59.155164 INFO::Formatting Data.
2025-03-23 20:13:59.155931 INFO::Recognized SummarizedExperiment
2025-03-23 20:13:59.156451 INFO::Typecasting input to dataframe.
2025-03-23 20:13:59.185764 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:59.186962 INFO::Removing potential empty rows and columns
2025-03-23 20:13:59.190369 INFO::Found 0 missing values.
2025-03-23 20:13:59.196573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:13:59.197143 INFO::Done
2025-03-23 20:13:59.19764 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:13:59.200934 INFO::Starting hierarchical adjustment
2025-03-23 20:13:59.201613 INFO::Found 2 batches.
2025-03-23 20:13:59.202123 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:13:59.203122 INFO::Using default BPPARAM
2025-03-23 20:13:59.203629 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:13:59.20454 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:13:59.266186 INFO::Done
2025-03-23 20:13:59.267044 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:13:59.270834 INFO::ASW Batch was 0.01078405383168 prior to batch effect correction and is now -0.090642492871253 .
2025-03-23 20:13:59.271777 INFO::Total function execution time is 0.116887331008911 s and adjustment time is 0.0645155906677246 s ( 55.19 )
2025-03-23 20:13:59.292279 INFO::Formatting Data.
2025-03-23 20:13:59.293036 INFO::Recognized SummarizedExperiment
2025-03-23 20:13:59.293591 INFO::Typecasting input to dataframe.
2025-03-23 20:13:59.303229 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:59.304377 INFO::Removing potential empty rows and columns
2025-03-23 20:13:59.308123 INFO::Found 0 missing values.
2025-03-23 20:13:59.315418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:13:59.316021 INFO::Done
2025-03-23 20:13:59.316558 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:13:59.32021 INFO::Starting hierarchical adjustment
2025-03-23 20:13:59.320964 INFO::Found 2 batches.
2025-03-23 20:13:59.321501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:13:59.322128 INFO::Using default BPPARAM
2025-03-23 20:13:59.322666 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:13:59.323655 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:13:59.349172 INFO::Done
2025-03-23 20:13:59.349896 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:13:59.353527 INFO::ASW Batch was 0.00261541368303127 prior to batch effect correction and is now 0.00261541368303127 .
2025-03-23 20:13:59.354371 INFO::Total function execution time is 0.0620725154876709 s and adjustment time is 0.0283324718475342 s ( 45.64 )
2025-03-23 20:13:59.372373 INFO::Formatting Data.
2025-03-23 20:13:59.373185 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:59.374114 INFO::Removing potential empty rows and columns
2025-03-23 20:13:59.375289 INFO::Found 0 missing values.
2025-03-23 20:13:59.378251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:13:59.378791 INFO::Done
2025-03-23 20:13:59.379332 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:13:59.381446 INFO::Starting hierarchical adjustment
2025-03-23 20:13:59.382164 INFO::Found 3 batches.
2025-03-23 20:13:59.382693 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:13:59.383327 INFO::Using default BPPARAM
2025-03-23 20:13:59.383877 INFO::Processing subtree level 1
2025-03-23 20:13:59.53514 INFO::Adjusting the last 1 batches sequentially
2025-03-23 20:13:59.537311 INFO::Done
2025-03-23 20:13:59.538108 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:13:59.540859 INFO::ASW Batch was -0.0932961349788583 prior to batch effect correction and is now -0.167083612011425 .
2025-03-23 20:13:59.541901 INFO::Total function execution time is 0.169522285461426 s and adjustment time is 0.155246019363403 s ( 91.58 )
2025-03-23 20:13:59.557789 INFO::Skipping initial DF formatting
2025-03-23 20:13:59.558598 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:13:59.562838 INFO::Starting hierarchical adjustment
2025-03-23 20:13:59.56374 INFO::Found 5 batches.
2025-03-23 20:13:59.564318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:13:59.565013 INFO::Using default BPPARAM
2025-03-23 20:13:59.56556 INFO::Processing subtree level 1
2025-03-23 20:13:59.693101 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:13:59.694921 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:13:59.715208 INFO::Done
2025-03-23 20:13:59.716048 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:13:59.720479 INFO::ASW Batch was 0.471986248799546 prior to batch effect correction and is now 0.471986248799546 .
2025-03-23 20:13:59.721184 INFO::ASW Label was 0.39900673195249 prior to batch effect correction and is now 0.39900673195249 .
2025-03-23 20:13:59.722097 INFO::Total function execution time is 0.164428472518921 s and adjustment time is 0.151628494262695 s ( 92.22 )
2025-03-23 20:13:59.740433 INFO::Formatting Data.
2025-03-23 20:13:59.741345 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:59.742372 INFO::Removing potential empty rows and columns
2025-03-23 20:13:59.743425 INFO::Found 0 missing values.
2025-03-23 20:13:59.747693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:13:59.748309 INFO::Done
2025-03-23 20:13:59.748873 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:13:59.751985 INFO::Starting hierarchical adjustment
2025-03-23 20:13:59.752733 INFO::Found 5 batches.
2025-03-23 20:13:59.753278 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:13:59.753964 INFO::Using default BPPARAM
2025-03-23 20:13:59.754507 INFO::Processing subtree level 1
2025-03-23 20:13:59.871316 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:13:59.873063 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:13:59.889316 INFO::Done
2025-03-23 20:13:59.8901 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:13:59.893537 INFO::ASW Batch was 0.422573412490404 prior to batch effect correction and is now -0.0721149698900773 .
2025-03-23 20:13:59.894175 INFO::ASW Label was 0.331253808016827 prior to batch effect correction and is now 0.788706031252922 .
2025-03-23 20:13:59.895019 INFO::Total function execution time is 0.154690742492676 s and adjustment time is 0.136713743209839 s ( 88.38 )
2025-03-23 20:13:59.895898 INFO::Formatting Data.
2025-03-23 20:13:59.896535 INFO::Replacing NaNs with NAs.
2025-03-23 20:13:59.89744 INFO::Removing potential empty rows and columns
2025-03-23 20:13:59.898476 INFO::Found 0 missing values.
2025-03-23 20:13:59.90273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:13:59.90329 INFO::Done
2025-03-23 20:13:59.903827 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:13:59.906959 INFO::Starting hierarchical adjustment
2025-03-23 20:13:59.90768 INFO::Found 5 batches.
2025-03-23 20:13:59.90824 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:13:59.908911 INFO::Using default BPPARAM
2025-03-23 20:13:59.909466 INFO::Processing subtree level 1
2025-03-23 20:14:00.024101 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:14:00.025856 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:14:00.041991 INFO::Done
2025-03-23 20:14:00.042858 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:00.046412 INFO::ASW Batch was 0.422573412490404 prior to batch effect correction and is now -0.0721149698900773 .
2025-03-23 20:14:00.047121 INFO::ASW Label was 0.331253808016827 prior to batch effect correction and is now 0.788706031252922 .
2025-03-23 20:14:00.048008 INFO::Total function execution time is 0.152092933654785 s and adjustment time is 0.13439679145813 s ( 88.36 )
2025-03-23 20:14:00.062307 INFO::Formatting Data.
2025-03-23 20:14:00.063196 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:00.06422 INFO::Removing potential empty rows and columns
2025-03-23 20:14:00.065305 INFO::Found 0 missing values.
2025-03-23 20:14:00.069571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:00.070212 INFO::Done
2025-03-23 20:14:00.070801 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:00.073985 INFO::Starting hierarchical adjustment
2025-03-23 20:14:00.074793 INFO::Found 5 batches.
2025-03-23 20:14:00.075389 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:00.076163 INFO::Using default BPPARAM
2025-03-23 20:14:00.076729 INFO::Processing subtree level 1
2025-03-23 20:14:00.197231 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:14:00.19906 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:14:00.215694 INFO::Done
2025-03-23 20:14:00.216529 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:00.219906 INFO::ASW Batch was 0.419418034859424 prior to batch effect correction and is now -0.0562835241466475 .
2025-03-23 20:14:00.220614 INFO::ASW Label was 0.424982792530897 prior to batch effect correction and is now 0.802675417635653 .
2025-03-23 20:14:00.221501 INFO::Total function execution time is 0.159311056137085 s and adjustment time is 0.141034603118896 s ( 88.53 )
2025-03-23 20:14:00.222426 INFO::Formatting Data.
2025-03-23 20:14:00.22309 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:00.224053 INFO::Removing potential empty rows and columns
2025-03-23 20:14:00.225108 INFO::Found 0 missing values.
2025-03-23 20:14:00.22938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:00.229973 INFO::Done
2025-03-23 20:14:00.230507 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:00.233654 INFO::Starting hierarchical adjustment
2025-03-23 20:14:00.234396 INFO::Found 5 batches.
2025-03-23 20:14:00.234953 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:00.235623 INFO::Using default BPPARAM
2025-03-23 20:14:00.236186 INFO::Processing subtree level 1
2025-03-23 20:14:00.357525 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:14:00.35932 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:14:00.375179 INFO::Done
2025-03-23 20:14:00.375938 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:00.379298 INFO::ASW Batch was 0.419418034859424 prior to batch effect correction and is now -0.0562835241466475 .
2025-03-23 20:14:00.379943 INFO::ASW Label was 0.424982792530897 prior to batch effect correction and is now 0.802675417635653 .
2025-03-23 20:14:00.380783 INFO::Total function execution time is 0.158368587493896 s and adjustment time is 0.140912294387817 s ( 88.98 )
2025-03-23 20:14:00.394542 INFO::Formatting Data.
2025-03-23 20:14:00.395327 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:00.396251 INFO::Removing potential empty rows and columns
2025-03-23 20:14:00.397303 INFO::Found 0 missing values.
2025-03-23 20:14:00.400084 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:00.400635 INFO::Done
2025-03-23 20:14:00.401176 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:00.404182 INFO::Starting hierarchical adjustment
2025-03-23 20:14:00.404904 INFO::Found 2 batches.
2025-03-23 20:14:00.405452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:00.406123 INFO::Using default BPPARAM
2025-03-23 20:14:00.406673 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:14:00.407595 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:14:00.422315 INFO::Done
2025-03-23 20:14:00.422977 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:00.425986 INFO::ASW Batch was 0.619210809310278 prior to batch effect correction and is now 0.0076190474533024 .
2025-03-23 20:14:00.426581 INFO::ASW Label was 0.443673950324275 prior to batch effect correction and is now 0.920133493828965 .
2025-03-23 20:14:00.427406 INFO::Total function execution time is 0.0329389572143555 s and adjustment time is 0.017561674118042 s ( 53.32 )
2025-03-23 20:14:00.428228 INFO::Formatting Data.
2025-03-23 20:14:00.428878 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:00.42976 INFO::Removing potential empty rows and columns
2025-03-23 20:14:00.430735 INFO::Found 0 missing values.
2025-03-23 20:14:00.433413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:00.433981 INFO::Done
2025-03-23 20:14:00.43451 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:00.437399 INFO::Starting hierarchical adjustment
2025-03-23 20:14:00.43812 INFO::Found 2 batches.
2025-03-23 20:14:00.438647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:00.439272 INFO::Using default BPPARAM
2025-03-23 20:14:00.439817 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:14:00.440739 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:14:00.455411 INFO::Done
2025-03-23 20:14:00.456096 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:00.459059 INFO::ASW Batch was 0.619210809310278 prior to batch effect correction and is now 0.0076190474533024 .
2025-03-23 20:14:00.459633 INFO::ASW Label was 0.443673950324275 prior to batch effect correction and is now 0.920133493828965 .
2025-03-23 20:14:00.460453 INFO::Total function execution time is 0.0322437286376953 s and adjustment time is 0.0174365043640137 s ( 54.08 )
2025-03-23 20:14:00.471359 INFO::Formatting Data.
2025-03-23 20:14:00.472315 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:00.473214 INFO::Removing potential empty rows and columns
2025-03-23 20:14:00.474138 INFO::Found 0 missing values.
2025-03-23 20:14:00.476268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:00.476829 INFO::Done
2025-03-23 20:14:00.477366 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:00.479319 INFO::Starting hierarchical adjustment
2025-03-23 20:14:00.480049 INFO::Found 2 batches.
2025-03-23 20:14:00.480583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:00.481216 INFO::Using default BPPARAM
2025-03-23 20:14:00.481748 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:14:00.482682 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:14:00.514352 INFO::Done
2025-03-23 20:14:00.51509 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:00.517149 INFO::ASW Batch was -0.13518537919033 prior to batch effect correction and is now -0.169356101875722 .
2025-03-23 20:14:00.517977 INFO::Total function execution time is 0.0466823577880859 s and adjustment time is 0.0344433784484863 s ( 73.78 )
2025-03-23 20:14:00.529794 INFO::Formatting Data.
2025-03-23 20:14:00.53059 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:00.531512 INFO::Removing potential empty rows and columns
2025-03-23 20:14:00.532534 INFO::Found 0 missing values.
2025-03-23 20:14:00.533717 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.
2025-03-23 20:14:00.538567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:00.539156 INFO::Done
2025-03-23 20:14:00.539696 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:00.542729 INFO::Starting hierarchical adjustment
2025-03-23 20:14:00.543449 INFO::Found 2 batches.
2025-03-23 20:14:00.544006 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:00.544615 INFO::Using default BPPARAM
2025-03-23 20:14:00.545156 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:14:00.546127 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:14:00.562932 INFO::Done
2025-03-23 20:14:00.563648 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:00.566858 INFO::ASW Batch was 0.641193596219162 prior to batch effect correction and is now 0.0403967262169166 .
2025-03-23 20:14:00.56747 INFO::ASW Label was 0.349972221634186 prior to batch effect correction and is now 0.892608641126325 .
2025-03-23 20:14:00.568295 INFO::Total function execution time is 0.0385777950286865 s and adjustment time is 0.0195987224578857 s ( 50.8 )
2025-03-23 20:14:00.569109 INFO::Formatting Data.
2025-03-23 20:14:00.569732 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:00.570675 INFO::Removing potential empty rows and columns
2025-03-23 20:14:00.571667 INFO::Found 0 missing values.
2025-03-23 20:14:00.572578 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.
2025-03-23 20:14:00.57715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:00.5777 INFO::Done
2025-03-23 20:14:00.578242 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:00.581206 INFO::Starting hierarchical adjustment
2025-03-23 20:14:00.581918 INFO::Found 2 batches.
2025-03-23 20:14:00.582455 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:00.583116 INFO::Using default BPPARAM
2025-03-23 20:14:00.583654 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:14:00.584629 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:14:00.660018 INFO::Done
2025-03-23 20:14:00.660724 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:00.663639 INFO::ASW Batch was 0.641193596219162 prior to batch effect correction and is now 0.0403967262169166 .
2025-03-23 20:14:00.664259 INFO::ASW Label was 0.349972221634186 prior to batch effect correction and is now 0.892608641126325 .
2025-03-23 20:14:00.665097 INFO::Total function execution time is 0.0959863662719727 s and adjustment time is 0.078211784362793 s ( 81.48 )
2025-03-23 20:14:00.861793 INFO::Formatting Data.
2025-03-23 20:14:00.862842 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:00.863815 INFO::Removing potential empty rows and columns
2025-03-23 20:14:00.864846 INFO::Found 0 missing values.
2025-03-23 20:14:00.867925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:00.868547 INFO::Done
2025-03-23 20:14:00.869078 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:00.871238 INFO::Starting hierarchical adjustment
2025-03-23 20:14:00.872023 INFO::Found 3 batches.
2025-03-23 20:14:00.872551 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:00.873182 INFO::Using default BPPARAM
2025-03-23 20:14:00.873714 INFO::Processing subtree level 1
2025-03-23 20:14:00.998481 INFO::Adjusting the last 1 batches sequentially
2025-03-23 20:14:01.000698 INFO::Done
2025-03-23 20:14:01.001484 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:01.004888 INFO::ASW Batch was -0.061166672900186 prior to batch effect correction and is now -0.061166672900186 .
2025-03-23 20:14:01.005926 INFO::Total function execution time is 0.144170522689819 s and adjustment time is 0.128791332244873 s ( 89.33 )
2025-03-23 20:14:01.00724 INFO::Formatting Data.
2025-03-23 20:14:01.007976 INFO::Typecasting input to dataframe.
2025-03-23 20:14:01.008784 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:01.009997 INFO::Removing potential empty rows and columns
2025-03-23 20:14:01.011367 INFO::Found 0 missing values.
2025-03-23 20:14:01.01508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:01.015698 INFO::Done
2025-03-23 20:14:01.016303 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:01.018577 INFO::Starting hierarchical adjustment
2025-03-23 20:14:01.019456 INFO::Found 3 batches.
2025-03-23 20:14:01.020358 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:01.021121 INFO::Using default BPPARAM
2025-03-23 20:14:01.021683 INFO::Processing subtree level 1
2025-03-23 20:14:01.121242 INFO::Adjusting the last 1 batches sequentially
2025-03-23 20:14:01.123715 INFO::Done
2025-03-23 20:14:01.124598 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:01.127448 INFO::ASW Batch was -0.061166672900186 prior to batch effect correction and is now -0.061166672900186 .
2025-03-23 20:14:01.12849 INFO::Total function execution time is 0.121252536773682 s and adjustment time is 0.104454755783081 s ( 86.15 )
2025-03-23 20:14:01.143811 INFO::Formatting Data.
2025-03-23 20:14:01.144674 INFO::Typecasting input to dataframe.
2025-03-23 20:14:01.145662 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:01.146654 INFO::Removing potential empty rows and columns
2025-03-23 20:14:01.147843 INFO::Found 0 missing values.
2025-03-23 20:14:01.150834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:01.151408 INFO::Done
2025-03-23 20:14:01.15195 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:01.154158 INFO::Starting hierarchical adjustment
2025-03-23 20:14:01.154989 INFO::Found 3 batches.
2025-03-23 20:14:01.155562 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:01.156304 INFO::Using default BPPARAM
2025-03-23 20:14:01.156892 INFO::Processing subtree level 1
2025-03-23 20:14:01.258908 INFO::Adjusting the last 1 batches sequentially
2025-03-23 20:14:01.260799 INFO::Done
2025-03-23 20:14:01.2615 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:01.264173 INFO::ASW Batch was -0.00759312009024911 prior to batch effect correction and is now -0.00759312009024911 .
2025-03-23 20:14:01.265168 INFO::Total function execution time is 0.121392011642456 s and adjustment time is 0.10596489906311 s ( 87.29 )
2025-03-23 20:14:01.419514 INFO::Formatting Data.
2025-03-23 20:14:01.420482 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:01.421759 INFO::Removing potential empty rows and columns
2025-03-23 20:14:01.424731 INFO::Found 1000 missing values.
2025-03-23 20:14:01.444445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:01.445284 INFO::Done
2025-03-23 20:14:01.44591 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:01.451797 INFO::Starting hierarchical adjustment
2025-03-23 20:14:01.452743 INFO::Found 10 batches.
2025-03-23 20:14:01.453382 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:01.454109 INFO::Using default BPPARAM
2025-03-23 20:14:01.454735 INFO::Processing subtree level 1
2025-03-23 20:14:01.612302 INFO::Processing subtree level 2
2025-03-23 20:14:01.782793 INFO::Adjusting the last 1 batches sequentially
2025-03-23 20:14:01.785175 INFO::Done
2025-03-23 20:14:01.785941 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:01.792071 INFO::ASW Batch was 0.534653267947476 prior to batch effect correction and is now 0.534653267947476 .
2025-03-23 20:14:01.792888 INFO::ASW Label was 0.31726903373767 prior to batch effect correction and is now 0.31726903373767 .
2025-03-23 20:14:01.793885 INFO::Total function execution time is 0.374425888061523 s and adjustment time is 0.332583904266357 s ( 88.83 )
2025-03-23 20:14:01.794888 INFO::Formatting Data.
2025-03-23 20:14:01.795591 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:01.797079 INFO::Removing potential empty rows and columns
2025-03-23 20:14:01.799853 INFO::Found 1000 missing values.
2025-03-23 20:14:01.81909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:01.819948 INFO::Done
2025-03-23 20:14:01.82055 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:01.826271 INFO::Starting hierarchical adjustment
2025-03-23 20:14:01.827142 INFO::Found 10 batches.
2025-03-23 20:14:03.242254 INFO::Set up parallel execution backend with 2 workers
2025-03-23 20:14:03.245112 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-23 20:14:04.462132 INFO::Adjusting the last 2 batches sequentially
2025-03-23 20:14:04.464224 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 20:14:04.480395 INFO::Done
2025-03-23 20:14:04.481035 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:04.485422 INFO::ASW Batch was 0.534653267947476 prior to batch effect correction and is now 0.534653267947476 .
2025-03-23 20:14:04.485981 INFO::ASW Label was 0.31726903373767 prior to batch effect correction and is now 0.31726903373767 .
2025-03-23 20:14:04.486742 INFO::Total function execution time is 2.69192790985107 s and adjustment time is 2.65344095230103 s ( 98.57 )
2025-03-23 20:14:04.643658 INFO::Formatting Data.
2025-03-23 20:14:04.644818 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:04.646176 INFO::Removing potential empty rows and columns
2025-03-23 20:14:04.647706 INFO::Found 0 missing values.
2025-03-23 20:14:04.653049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:04.653844 INFO::Done
2025-03-23 20:14:04.654607 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 20:14:04.657889 INFO::Starting hierarchical adjustment
2025-03-23 20:14:04.658589 INFO::Found 3 batches.
2025-03-23 20:14:04.659121 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 20:14:04.659752 INFO::Using default BPPARAM
2025-03-23 20:14:04.660399 INFO::Processing subtree level 1
2025-03-23 20:14:04.780749 INFO::Adjusting the last 1 batches sequentially
2025-03-23 20:14:04.783264 INFO::Done
2025-03-23 20:14:04.784137 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 20:14:04.787959 INFO::ASW Batch was 0.19338597187089 prior to batch effect correction and is now -0.151457738657599 .
2025-03-23 20:14:04.78875 INFO::ASW Label was -0.154279145732377 prior to batch effect correction and is now 0.105957991043889 .
2025-03-23 20:14:04.789953 INFO::Total function execution time is 0.146388292312622 s and adjustment time is 0.124753713607788 s ( 85.22 )
2025-03-23 20:14:04.936882 INFO::Formatting Data.
2025-03-23 20:14:04.937806 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:04.938786 INFO::Removing potential empty rows and columns
2025-03-23 20:14:04.939913 INFO::Found 2 missing values.
2025-03-23 20:14:04.942895 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:04.943456 INFO::Done
2025-03-23 20:14:04.972099 INFO::Found NA in Reference column
2025-03-23 20:14:04.981841 INFO::Require at least two references per batch.
2025-03-23 20:14:05.002417 INFO::Formatting Data.
2025-03-23 20:14:05.003321 INFO::Recognized SummarizedExperiment
2025-03-23 20:14:05.003914 INFO::Typecasting input to dataframe.
2025-03-23 20:14:05.014199 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:05.015536 INFO::Removing potential empty rows and columns
2025-03-23 20:14:05.019193 INFO::Found 0 missing values.
2025-03-23 20:14:05.026305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:05.026957 INFO::Done
2025-03-23 20:14:05.042854 INFO::Formatting Data.
2025-03-23 20:14:05.043607 INFO::Recognized SummarizedExperiment
2025-03-23 20:14:05.044171 INFO::Typecasting input to dataframe.
2025-03-23 20:14:05.062555 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:05.066338 INFO::Removing potential empty rows and columns
2025-03-23 20:14:05.070366 INFO::Found 0 missing values.
2025-03-23 20:14:05.081902 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:05.082676 INFO::Done
2025-03-23 20:14:05.099735 INFO::Formatting Data.
2025-03-23 20:14:05.100625 INFO::Recognized SummarizedExperiment
2025-03-23 20:14:05.101235 INFO::Typecasting input to dataframe.
2025-03-23 20:14:05.119448 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:05.120622 INFO::Removing potential empty rows and columns
2025-03-23 20:14:05.121779 INFO::Found 0 missing values.
2025-03-23 20:14:05.122807 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.
2025-03-23 20:14:05.127669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:05.128268 INFO::Done
2025-03-23 20:14:05.13994 INFO::Formatting Data.
2025-03-23 20:14:05.140909 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:05.141904 INFO::Removing potential empty rows and columns
2025-03-23 20:14:05.143028 INFO::Found 0 missing values.
2025-03-23 20:14:05.146104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:05.146676 INFO::Done
2025-03-23 20:14:05.159017 INFO::Formatting Data.
2025-03-23 20:14:05.159837 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:05.160781 INFO::Removing potential empty rows and columns
2025-03-23 20:14:05.161876 INFO::Found 0 missing values.
2025-03-23 20:14:05.164851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:05.165455 INFO::Done
2025-03-23 20:14:05.196444 INFO::Formatting Data.
2025-03-23 20:14:05.197387 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:05.198535 INFO::Removing potential empty rows and columns
2025-03-23 20:14:05.199815 INFO::Found 1 missing values.
2025-03-23 20:14:05.202617 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:05.203236 INFO::Done
2025-03-23 20:14:05.22436 INFO::Formatting Data.
2025-03-23 20:14:05.225319 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:05.226272 INFO::Removing potential empty rows and columns
2025-03-23 20:14:05.227238 INFO::Found 2 missing values.
2025-03-23 20:14:05.228139 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.
2025-03-23 20:14:05.23036 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:05.230922 INFO::Done
2025-03-23 20:14:05.240297 INFO::Formatting Data.
2025-03-23 20:14:05.241156 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:05.242045 INFO::Removing potential empty rows and columns
2025-03-23 20:14:05.242934 INFO::Found 2 missing values.
2025-03-23 20:14:05.244447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:05.244974 INFO::Done
2025-03-23 20:14:05.254719 INFO::Formatting Data.
2025-03-23 20:14:05.255482 INFO::Typecasting input to dataframe.
2025-03-23 20:14:05.256279 INFO::Replacing NaNs with NAs.
2025-03-23 20:14:05.257133 INFO::Removing potential empty rows and columns
2025-03-23 20:14:05.258112 INFO::Found 0 missing values.
2025-03-23 20:14:05.260913 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 20:14:05.261449 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.445 4.298 21.372
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.061 | 1.306 | 17.918 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.014 | 0.001 | 0.015 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |