Yannis Schumann
| Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2024-11-08 21:00:03 -0500 (Fri, 08 Nov 2024) |
| EndedAt: 2024-11-08 21:04:12 -0500 (Fri, 08 Nov 2024) |
| EllapsedTime: 248.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 8.245 0.247 5.856
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-11-08 21:04:06.034421 INFO::Formatting Data.
2024-11-08 21:04:06.035789 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:06.039709 INFO::Removing potential empty rows and columns
2024-11-08 21:04:06.13355 INFO::Found 0 missing values.
2024-11-08 21:04:06.13463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:06.134812 INFO::Done
2024-11-08 21:04:06.134973 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:06.139646 INFO::Starting hierarchical adjustment
2024-11-08 21:04:06.139898 INFO::Found 3 batches.
2024-11-08 21:04:06.140071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:06.140406 INFO::Using default BPPARAM
2024-11-08 21:04:06.140557 INFO::Processing subtree level 1
2024-11-08 21:04:06.175013 INFO::Adjusting the last 1 batches sequentially
2024-11-08 21:04:06.175914 INFO::Done
2024-11-08 21:04:06.176122 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:06.177447 INFO::ASW Batch was -0.0365886707584642 prior to batch effect correction and is now -0.0365886707584642 .
2024-11-08 21:04:06.177954 INFO::Total function execution time is 0.14385199546814 s and adjustment time is 0.0360691547393799 s ( 25.07 )
2024-11-08 21:04:06.183641 INFO::Formatting Data.
2024-11-08 21:04:06.183864 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:06.18414 INFO::Removing potential empty rows and columns
2024-11-08 21:04:06.184478 INFO::Found 0 missing values.
2024-11-08 21:04:06.184761 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-11-08 21:04:06.18831 INFO::Formatting Data.
2024-11-08 21:04:06.188515 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:06.188778 INFO::Removing potential empty rows and columns
2024-11-08 21:04:06.189071 INFO::Found 0 missing values.
2024-11-08 21:04:06.189336 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-11-08 21:04:06.19445 INFO::Formatting Data.
2024-11-08 21:04:06.194665 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:06.194925 INFO::Removing potential empty rows and columns
2024-11-08 21:04:06.195235 INFO::Found 0 missing values.
2024-11-08 21:04:06.195555 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-11-08 21:04:06.196954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:06.197115 INFO::Done
2024-11-08 21:04:06.197273 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:06.197879 INFO::Starting hierarchical adjustment
2024-11-08 21:04:06.198071 INFO::Found 2 batches.
2024-11-08 21:04:06.198215 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:06.198425 INFO::Using default BPPARAM
2024-11-08 21:04:06.198563 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:06.198817 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:06.206667 INFO::Done
2024-11-08 21:04:06.206872 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:06.207504 INFO::ASW Batch was -0.0255988591040215 prior to batch effect correction and is now -0.120747601439967 .
2024-11-08 21:04:06.207741 INFO::Total function execution time is 0.0132999420166016 s and adjustment time is 0.0086209774017334 s ( 64.82 )
2024-11-08 21:04:06.208708 INFO::Formatting Data.
2024-11-08 21:04:06.208877 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:06.211508 INFO::Formatting Data.
2024-11-08 21:04:06.2117 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:06.211943 INFO::Removing potential empty rows and columns
2024-11-08 21:04:06.212244 INFO::Found 0 missing values.
2024-11-08 21:04:06.213032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:06.213183 INFO::Done
2024-11-08 21:04:06.213319 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:06.213869 INFO::Starting hierarchical adjustment
2024-11-08 21:04:06.214051 INFO::Found 2 batches.
2024-11-08 21:04:06.214186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:06.214349 INFO::Using default BPPARAM
2024-11-08 21:04:06.21448 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:06.21477 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:06.219131 INFO::Done
2024-11-08 21:04:06.219311 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:06.219859 INFO::ASW Batch was -0.00135917783076716 prior to batch effect correction and is now -0.117010867570426 .
2024-11-08 21:04:06.22009 INFO::Total function execution time is 0.00857210159301758 s and adjustment time is 0.00511503219604492 s ( 59.67 )
2024-11-08 21:04:06.220375 INFO::Formatting Data.
2024-11-08 21:04:06.220532 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:06.220758 INFO::Removing potential empty rows and columns
2024-11-08 21:04:06.221023 INFO::Found 0 missing values.
2024-11-08 21:04:06.221797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:06.221945 INFO::Done
2024-11-08 21:04:06.222085 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:06.222597 INFO::Starting hierarchical adjustment
2024-11-08 21:04:06.222776 INFO::Found 2 batches.
2024-11-08 21:04:06.222908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:06.223065 INFO::Using default BPPARAM
2024-11-08 21:04:06.223194 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:06.223421 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:06.227579 INFO::Done
2024-11-08 21:04:06.227754 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:06.228303 INFO::ASW Batch was -0.00135917783076716 prior to batch effect correction and is now -0.117010867570426 .
2024-11-08 21:04:06.228514 INFO::Total function execution time is 0.00813102722167969 s and adjustment time is 0.00483798980712891 s ( 59.5 )
2024-11-08 21:04:07.354382 INFO::Formatting Data.
2024-11-08 21:04:07.354617 INFO::Recognized SummarizedExperiment
2024-11-08 21:04:07.354749 INFO::Typecasting input to dataframe.
2024-11-08 21:04:07.363762 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.364094 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.365034 INFO::Found 0 missing values.
2024-11-08 21:04:07.366844 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.366979 INFO::Done
2024-11-08 21:04:07.367107 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.368164 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.368344 INFO::Found 2 batches.
2024-11-08 21:04:07.368474 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.368741 INFO::Using default BPPARAM
2024-11-08 21:04:07.368869 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.369116 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.383661 INFO::Done
2024-11-08 21:04:07.383869 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.384911 INFO::ASW Batch was 0.0151269089649601 prior to batch effect correction and is now -0.0954662925967349 .
2024-11-08 21:04:07.38513 INFO::Total function execution time is 0.0308401584625244 s and adjustment time is 0.0153470039367676 s ( 49.76 )
2024-11-08 21:04:07.390427 INFO::Formatting Data.
2024-11-08 21:04:07.390609 INFO::Recognized SummarizedExperiment
2024-11-08 21:04:07.390746 INFO::Typecasting input to dataframe.
2024-11-08 21:04:07.393324 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.393623 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.394637 INFO::Found 0 missing values.
2024-11-08 21:04:07.396534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.396671 INFO::Done
2024-11-08 21:04:07.396801 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.397818 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.397999 INFO::Found 2 batches.
2024-11-08 21:04:07.398129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.398282 INFO::Using default BPPARAM
2024-11-08 21:04:07.398405 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.398652 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.405702 INFO::Done
2024-11-08 21:04:07.405874 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.406898 INFO::ASW Batch was 0.0240380353601693 prior to batch effect correction and is now 0.0240380353601693 .
2024-11-08 21:04:07.407113 INFO::Total function execution time is 0.0166749954223633 s and adjustment time is 0.0077369213104248 s ( 46.4 )
2024-11-08 21:04:07.412474 INFO::Formatting Data.
2024-11-08 21:04:07.412662 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.412885 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.413144 INFO::Found 0 missing values.
2024-11-08 21:04:07.413896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.414031 INFO::Done
2024-11-08 21:04:07.414161 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.414676 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.414842 INFO::Found 3 batches.
2024-11-08 21:04:07.414968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.415115 INFO::Using default BPPARAM
2024-11-08 21:04:07.415245 INFO::Processing subtree level 1
2024-11-08 21:04:07.46652 INFO::Adjusting the last 1 batches sequentially
2024-11-08 21:04:07.467681 INFO::Done
2024-11-08 21:04:07.467948 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.469349 INFO::ASW Batch was 0.0150123050088613 prior to batch effect correction and is now -0.155792050423344 .
2024-11-08 21:04:07.469812 INFO::Total function execution time is 0.057326078414917 s and adjustment time is 0.0528709888458252 s ( 92.23 )
2024-11-08 21:04:07.475037 INFO::Skipping initial DF formatting
2024-11-08 21:04:07.475234 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.47641 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.476622 INFO::Found 5 batches.
2024-11-08 21:04:07.476762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.476946 INFO::Using default BPPARAM
2024-11-08 21:04:07.47708 INFO::Processing subtree level 1
2024-11-08 21:04:07.513896 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.514739 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.520893 INFO::Done
2024-11-08 21:04:07.521177 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.522879 INFO::ASW Batch was 0.557365569974428 prior to batch effect correction and is now 0.557365569974428 .
2024-11-08 21:04:07.52305 INFO::ASW Label was 0.334572895779479 prior to batch effect correction and is now 0.334572895779479 .
2024-11-08 21:04:07.523419 INFO::Total function execution time is 0.048386812210083 s and adjustment time is 0.0443148612976074 s ( 91.58 )
2024-11-08 21:04:07.529191 INFO::Formatting Data.
2024-11-08 21:04:07.52939 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.529645 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.529937 INFO::Found 0 missing values.
2024-11-08 21:04:07.530977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.531119 INFO::Done
2024-11-08 21:04:07.531267 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.532027 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.532215 INFO::Found 5 batches.
2024-11-08 21:04:07.532349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.532609 INFO::Using default BPPARAM
2024-11-08 21:04:07.532743 INFO::Processing subtree level 1
2024-11-08 21:04:07.564085 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.565368 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.572594 INFO::Done
2024-11-08 21:04:07.572769 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.573889 INFO::ASW Batch was 0.330408467586888 prior to batch effect correction and is now -0.0310510309049437 .
2024-11-08 21:04:07.574054 INFO::ASW Label was 0.465540809114901 prior to batch effect correction and is now 0.755492681041974 .
2024-11-08 21:04:07.57443 INFO::Total function execution time is 0.0452420711517334 s and adjustment time is 0.040416955947876 s ( 89.33 )
2024-11-08 21:04:07.574661 INFO::Formatting Data.
2024-11-08 21:04:07.574813 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.575039 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.5753 INFO::Found 0 missing values.
2024-11-08 21:04:07.576321 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.576464 INFO::Done
2024-11-08 21:04:07.576594 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.57735 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.577639 INFO::Found 5 batches.
2024-11-08 21:04:07.577789 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.577986 INFO::Using default BPPARAM
2024-11-08 21:04:07.578203 INFO::Processing subtree level 1
2024-11-08 21:04:07.608089 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.609296 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.616178 INFO::Done
2024-11-08 21:04:07.616403 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.617562 INFO::ASW Batch was 0.330408467586888 prior to batch effect correction and is now -0.0310510309049437 .
2024-11-08 21:04:07.61775 INFO::ASW Label was 0.465540809114901 prior to batch effect correction and is now 0.755492681041974 .
2024-11-08 21:04:07.618224 INFO::Total function execution time is 0.043532133102417 s and adjustment time is 0.0386419296264648 s ( 88.77 )
2024-11-08 21:04:07.623487 INFO::Formatting Data.
2024-11-08 21:04:07.6237 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.623966 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.624264 INFO::Found 0 missing values.
2024-11-08 21:04:07.625429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.625598 INFO::Done
2024-11-08 21:04:07.625746 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.626618 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.626826 INFO::Found 5 batches.
2024-11-08 21:04:07.626971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.627164 INFO::Using default BPPARAM
2024-11-08 21:04:07.627305 INFO::Processing subtree level 1
2024-11-08 21:04:07.658486 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.65967 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.666929 INFO::Done
2024-11-08 21:04:07.667171 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.668388 INFO::ASW Batch was 0.441333189361629 prior to batch effect correction and is now -0.0629260820636361 .
2024-11-08 21:04:07.668579 INFO::ASW Label was 0.386964463229288 prior to batch effect correction and is now 0.85509589188012 .
2024-11-08 21:04:07.669269 INFO::Total function execution time is 0.0457720756530762 s and adjustment time is 0.0401380062103271 s ( 87.69 )
2024-11-08 21:04:07.669546 INFO::Formatting Data.
2024-11-08 21:04:07.669725 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.669983 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.6703 INFO::Found 0 missing values.
2024-11-08 21:04:07.67146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.671631 INFO::Done
2024-11-08 21:04:07.671785 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.672681 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.672927 INFO::Found 5 batches.
2024-11-08 21:04:07.673077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.67328 INFO::Using default BPPARAM
2024-11-08 21:04:07.673594 INFO::Processing subtree level 1
2024-11-08 21:04:07.707784 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.709237 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.716158 INFO::Done
2024-11-08 21:04:07.716385 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.717614 INFO::ASW Batch was 0.441333189361629 prior to batch effect correction and is now -0.0629260820636361 .
2024-11-08 21:04:07.717794 INFO::ASW Label was 0.386964463229288 prior to batch effect correction and is now 0.85509589188012 .
2024-11-08 21:04:07.718179 INFO::Total function execution time is 0.0486011505126953 s and adjustment time is 0.0432710647583008 s ( 89.03 )
2024-11-08 21:04:07.723732 INFO::Formatting Data.
2024-11-08 21:04:07.723973 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.724259 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.724589 INFO::Found 0 missing values.
2024-11-08 21:04:07.72541 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.725575 INFO::Done
2024-11-08 21:04:07.725726 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.726638 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.726849 INFO::Found 2 batches.
2024-11-08 21:04:07.726992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.727196 INFO::Using default BPPARAM
2024-11-08 21:04:07.727361 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.727617 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.732188 INFO::Done
2024-11-08 21:04:07.732404 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.733268 INFO::ASW Batch was 0.5159127227289 prior to batch effect correction and is now 0.0361498546115553 .
2024-11-08 21:04:07.733434 INFO::ASW Label was 0.567111880272176 prior to batch effect correction and is now 0.907040872610981 .
2024-11-08 21:04:07.733676 INFO::Total function execution time is 0.00998210906982422 s and adjustment time is 0.00538206100463867 s ( 53.92 )
2024-11-08 21:04:07.733893 INFO::Formatting Data.
2024-11-08 21:04:07.734056 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.734286 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.734558 INFO::Found 0 missing values.
2024-11-08 21:04:07.735303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.735457 INFO::Done
2024-11-08 21:04:07.735608 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.736408 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.736734 INFO::Found 2 batches.
2024-11-08 21:04:07.736879 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.737044 INFO::Using default BPPARAM
2024-11-08 21:04:07.73718 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.737422 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.741705 INFO::Done
2024-11-08 21:04:07.741895 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.742776 INFO::ASW Batch was 0.5159127227289 prior to batch effect correction and is now 0.0361498546115553 .
2024-11-08 21:04:07.74295 INFO::ASW Label was 0.567111880272176 prior to batch effect correction and is now 0.907040872610981 .
2024-11-08 21:04:07.74318 INFO::Total function execution time is 0.0092780590057373 s and adjustment time is 0.00500607490539551 s ( 53.96 )
2024-11-08 21:04:07.747315 INFO::Formatting Data.
2024-11-08 21:04:07.747533 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.747779 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.748028 INFO::Found 0 missing values.
2024-11-08 21:04:07.748614 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.74877 INFO::Done
2024-11-08 21:04:07.748908 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.749453 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.749634 INFO::Found 2 batches.
2024-11-08 21:04:07.749775 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.749946 INFO::Using default BPPARAM
2024-11-08 21:04:07.750081 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.750319 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.760635 INFO::Done
2024-11-08 21:04:07.76085 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.761434 INFO::ASW Batch was 0.236731604266252 prior to batch effect correction and is now -0.166938288107475 .
2024-11-08 21:04:07.7618 INFO::Total function execution time is 0.0145020484924316 s and adjustment time is 0.0110259056091309 s ( 76.03 )
2024-11-08 21:04:07.765966 INFO::Formatting Data.
2024-11-08 21:04:07.76619 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.766443 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.766738 INFO::Found 0 missing values.
2024-11-08 21:04:07.767146 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-11-08 21:04:07.768452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.768616 INFO::Done
2024-11-08 21:04:07.768773 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.7696 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.769795 INFO::Found 2 batches.
2024-11-08 21:04:07.769941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.770113 INFO::Using default BPPARAM
2024-11-08 21:04:07.770245 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.770498 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.77554 INFO::Done
2024-11-08 21:04:07.775746 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.776602 INFO::ASW Batch was 0.465668772819303 prior to batch effect correction and is now -0.0234366729231993 .
2024-11-08 21:04:07.776795 INFO::ASW Label was 0.621917405207267 prior to batch effect correction and is now 0.945539828110257 .
2024-11-08 21:04:07.777016 INFO::Total function execution time is 0.0110740661621094 s and adjustment time is 0.00577306747436523 s ( 52.13 )
2024-11-08 21:04:07.77723 INFO::Formatting Data.
2024-11-08 21:04:07.777392 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.777641 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.777922 INFO::Found 0 missing values.
2024-11-08 21:04:07.778167 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-11-08 21:04:07.779441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.779599 INFO::Done
2024-11-08 21:04:07.779739 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.780547 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.78074 INFO::Found 2 batches.
2024-11-08 21:04:07.780881 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.781045 INFO::Using default BPPARAM
2024-11-08 21:04:07.781177 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:07.781428 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:07.786348 INFO::Done
2024-11-08 21:04:07.786544 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.787415 INFO::ASW Batch was 0.465668772819303 prior to batch effect correction and is now -0.0234366729231993 .
2024-11-08 21:04:07.787588 INFO::ASW Label was 0.621917405207267 prior to batch effect correction and is now 0.945539828110257 .
2024-11-08 21:04:07.787831 INFO::Total function execution time is 0.0105838775634766 s and adjustment time is 0.00563693046569824 s ( 53.26 )
2024-11-08 21:04:07.850715 INFO::Formatting Data.
2024-11-08 21:04:07.851103 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.851389 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.851699 INFO::Found 0 missing values.
2024-11-08 21:04:07.852561 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.852721 INFO::Done
2024-11-08 21:04:07.852876 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.853517 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.853713 INFO::Found 3 batches.
2024-11-08 21:04:07.853857 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.854036 INFO::Using default BPPARAM
2024-11-08 21:04:07.854193 INFO::Processing subtree level 1
2024-11-08 21:04:07.889015 INFO::Adjusting the last 1 batches sequentially
2024-11-08 21:04:07.890483 INFO::Done
2024-11-08 21:04:07.8907 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.892415 INFO::ASW Batch was 0.0541159860643929 prior to batch effect correction and is now 0.0541159860643929 .
2024-11-08 21:04:07.89295 INFO::Total function execution time is 0.0422430038452148 s and adjustment time is 0.0368080139160156 s ( 87.13 )
2024-11-08 21:04:07.893349 INFO::Formatting Data.
2024-11-08 21:04:07.893546 INFO::Typecasting input to dataframe.
2024-11-08 21:04:07.893773 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.894081 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.894501 INFO::Found 0 missing values.
2024-11-08 21:04:07.895578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.895745 INFO::Done
2024-11-08 21:04:07.895925 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.896523 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.896721 INFO::Found 3 batches.
2024-11-08 21:04:07.896874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.897063 INFO::Using default BPPARAM
2024-11-08 21:04:07.897203 INFO::Processing subtree level 1
2024-11-08 21:04:07.927073 INFO::Adjusting the last 1 batches sequentially
2024-11-08 21:04:07.927971 INFO::Done
2024-11-08 21:04:07.92815 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:07.929497 INFO::ASW Batch was 0.0541159860643929 prior to batch effect correction and is now 0.0541159860643929 .
2024-11-08 21:04:07.929913 INFO::Total function execution time is 0.0365610122680664 s and adjustment time is 0.0312910079956055 s ( 85.59 )
2024-11-08 21:04:07.934946 INFO::Formatting Data.
2024-11-08 21:04:07.935192 INFO::Typecasting input to dataframe.
2024-11-08 21:04:07.935439 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:07.93572 INFO::Removing potential empty rows and columns
2024-11-08 21:04:07.936068 INFO::Found 0 missing values.
2024-11-08 21:04:07.936906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:07.937066 INFO::Done
2024-11-08 21:04:07.937217 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:07.937806 INFO::Starting hierarchical adjustment
2024-11-08 21:04:07.938011 INFO::Found 3 batches.
2024-11-08 21:04:07.938266 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:07.938456 INFO::Using default BPPARAM
2024-11-08 21:04:07.938601 INFO::Processing subtree level 1
2024-11-08 21:04:08.015873 INFO::Adjusting the last 1 batches sequentially
2024-11-08 21:04:08.016988 INFO::Done
2024-11-08 21:04:08.017198 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:08.021191 INFO::ASW Batch was -0.101223731862363 prior to batch effect correction and is now -0.101223731862363 .
2024-11-08 21:04:08.022181 INFO::Total function execution time is 0.0871419906616211 s and adjustment time is 0.0790121555328369 s ( 90.67 )
2024-11-08 21:04:08.113439 INFO::Formatting Data.
2024-11-08 21:04:08.113717 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:08.114114 INFO::Removing potential empty rows and columns
2024-11-08 21:04:08.115054 INFO::Found 1000 missing values.
2024-11-08 21:04:08.121746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:08.121967 INFO::Done
2024-11-08 21:04:08.122159 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:08.124061 INFO::Starting hierarchical adjustment
2024-11-08 21:04:08.124291 INFO::Found 10 batches.
2024-11-08 21:04:08.124451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:08.124684 INFO::Using default BPPARAM
2024-11-08 21:04:08.12484 INFO::Processing subtree level 1
2024-11-08 21:04:08.173451 INFO::Processing subtree level 2
2024-11-08 21:04:08.232793 INFO::Adjusting the last 1 batches sequentially
2024-11-08 21:04:08.234106 INFO::Done
2024-11-08 21:04:08.23429 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:08.236969 INFO::ASW Batch was 0.476048256892145 prior to batch effect correction and is now 0.476048256892145 .
2024-11-08 21:04:08.237187 INFO::ASW Label was 0.327069311463335 prior to batch effect correction and is now 0.327069311463335 .
2024-11-08 21:04:08.237699 INFO::Total function execution time is 0.124271869659424 s and adjustment time is 0.10985803604126 s ( 88.4 )
2024-11-08 21:04:08.237975 INFO::Formatting Data.
2024-11-08 21:04:08.238154 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:08.238502 INFO::Removing potential empty rows and columns
2024-11-08 21:04:08.239421 INFO::Found 1000 missing values.
2024-11-08 21:04:08.245047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:08.245246 INFO::Done
2024-11-08 21:04:08.245417 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:08.24746 INFO::Starting hierarchical adjustment
2024-11-08 21:04:08.2477 INFO::Found 10 batches.
2024-11-08 21:04:08.622892 INFO::Set up parallel execution backend with 2 workers
2024-11-08 21:04:08.623193 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-11-08 21:04:09.045624 INFO::Adjusting the last 2 batches sequentially
2024-11-08 21:04:09.046115 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-08 21:04:09.051275 INFO::Done
2024-11-08 21:04:09.051458 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:09.053051 INFO::ASW Batch was 0.476048256892145 prior to batch effect correction and is now 0.476048256892145 .
2024-11-08 21:04:09.053198 INFO::ASW Label was 0.327069311463335 prior to batch effect correction and is now 0.327069311463335 .
2024-11-08 21:04:09.0534 INFO::Total function execution time is 0.815430879592896 s and adjustment time is 0.803623914718628 s ( 98.55 )
2024-11-08 21:04:09.104227 INFO::Formatting Data.
2024-11-08 21:04:09.104433 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.104727 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.105074 INFO::Found 0 missing values.
2024-11-08 21:04:09.106098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.106247 INFO::Done
2024-11-08 21:04:09.106379 INFO::Acquiring quality metrics before batch effect correction.
2024-11-08 21:04:09.107126 INFO::Starting hierarchical adjustment
2024-11-08 21:04:09.107317 INFO::Found 3 batches.
2024-11-08 21:04:09.107456 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-08 21:04:09.107634 INFO::Using default BPPARAM
2024-11-08 21:04:09.107772 INFO::Processing subtree level 1
2024-11-08 21:04:09.145361 INFO::Adjusting the last 1 batches sequentially
2024-11-08 21:04:09.163547 INFO::Done
2024-11-08 21:04:09.164146 INFO::Acquiring quality metrics after batch effect correction.
2024-11-08 21:04:09.165942 INFO::ASW Batch was 0.279290271252035 prior to batch effect correction and is now -0.13080597384848 .
2024-11-08 21:04:09.166284 INFO::ASW Label was -0.180396965625177 prior to batch effect correction and is now 0.017929870906884 .
2024-11-08 21:04:09.166743 INFO::Total function execution time is 0.0625100135803223 s and adjustment time is 0.0562498569488525 s ( 89.99 )
2024-11-08 21:04:09.208755 INFO::Formatting Data.
2024-11-08 21:04:09.209051 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.209504 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.209875 INFO::Found 2 missing values.
2024-11-08 21:04:09.210804 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.210976 INFO::Done
2024-11-08 21:04:09.221011 INFO::Found NA in Reference column
2024-11-08 21:04:09.224429 INFO::Require at least two references per batch.
2024-11-08 21:04:09.232015 INFO::Formatting Data.
2024-11-08 21:04:09.232232 INFO::Recognized SummarizedExperiment
2024-11-08 21:04:09.232392 INFO::Typecasting input to dataframe.
2024-11-08 21:04:09.2367 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.2371 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.238508 INFO::Found 0 missing values.
2024-11-08 21:04:09.241122 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.241292 INFO::Done
2024-11-08 21:04:09.246475 INFO::Formatting Data.
2024-11-08 21:04:09.246717 INFO::Recognized SummarizedExperiment
2024-11-08 21:04:09.246887 INFO::Typecasting input to dataframe.
2024-11-08 21:04:09.252753 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.253168 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.254442 INFO::Found 0 missing values.
2024-11-08 21:04:09.258676 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.258895 INFO::Done
2024-11-08 21:04:09.264672 INFO::Formatting Data.
2024-11-08 21:04:09.264915 INFO::Recognized SummarizedExperiment
2024-11-08 21:04:09.265101 INFO::Typecasting input to dataframe.
2024-11-08 21:04:09.271461 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.271827 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.272235 INFO::Found 0 missing values.
2024-11-08 21:04:09.272545 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-11-08 21:04:09.274243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.274419 INFO::Done
2024-11-08 21:04:09.27859 INFO::Formatting Data.
2024-11-08 21:04:09.278824 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.279093 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.279393 INFO::Found 0 missing values.
2024-11-08 21:04:09.280265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.280414 INFO::Done
2024-11-08 21:04:09.284219 INFO::Formatting Data.
2024-11-08 21:04:09.284442 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.284696 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.284988 INFO::Found 0 missing values.
2024-11-08 21:04:09.285837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.285999 INFO::Done
2024-11-08 21:04:09.295983 INFO::Formatting Data.
2024-11-08 21:04:09.296211 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.296503 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.296834 INFO::Found 1 missing values.
2024-11-08 21:04:09.297569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.297722 INFO::Done
2024-11-08 21:04:09.303809 INFO::Formatting Data.
2024-11-08 21:04:09.304046 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.304296 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.304571 INFO::Found 2 missing values.
2024-11-08 21:04:09.304825 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-11-08 21:04:09.305504 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.305658 INFO::Done
2024-11-08 21:04:09.309032 INFO::Formatting Data.
2024-11-08 21:04:09.309309 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.309581 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.309829 INFO::Found 2 missing values.
2024-11-08 21:04:09.310279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.310429 INFO::Done
2024-11-08 21:04:09.313937 INFO::Formatting Data.
2024-11-08 21:04:09.31416 INFO::Typecasting input to dataframe.
2024-11-08 21:04:09.314384 INFO::Replacing NaNs with NAs.
2024-11-08 21:04:09.314637 INFO::Removing potential empty rows and columns
2024-11-08 21:04:09.314938 INFO::Found 0 missing values.
2024-11-08 21:04:09.315792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-08 21:04:09.315959 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
5.999 1.053 7.198
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.245 | 0.247 | 5.856 | |
| compute_asw | 0.008 | 0.000 | 0.009 | |
| count_existing | 0.004 | 0.001 | 0.004 | |
| generate_data_covariables | 0.003 | 0.000 | 0.004 | |
| generate_dataset | 0.004 | 0.000 | 0.003 | |