Yannis Schumann
| Snapshot Date: 2024-11-20 13:40 -0500 (Wed, 20 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 10fd252 |
| git_last_commit_date: 2024-11-20 10:26:09 -0500 (Wed, 20 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-21 11:33 -0500 (Thu, 21 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4456 |
| 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 158/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.3 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | 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: 1.3.3 |
| 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_1.3.3.tar.gz |
| StartedAt: 2024-11-20 20:19:39 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 20:24:40 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 300.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BERT.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.3.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.3’
* 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 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 ... WARNING
Undocumented code objects:
‘generate_truncated_dataset’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 20.506 1.07 14.713
* 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: 1 WARNING
See
‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck/00check.log’
for details.
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’ ... ** 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) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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")
2024-11-20 20:24:06.595505 INFO::Formatting Data.
2024-11-20 20:24:06.596626 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:06.606718 INFO::Removing potential empty rows and columns
2024-11-20 20:24:06.822661 INFO::Found 0 missing values.
2024-11-20 20:24:06.82571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:06.826282 INFO::Done
2024-11-20 20:24:06.826771 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:06.836975 INFO::Starting hierarchical adjustment
2024-11-20 20:24:06.837739 INFO::Found 3 batches.
2024-11-20 20:24:06.838274 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:06.839307 INFO::Using default BPPARAM
2024-11-20 20:24:06.839834 INFO::Processing subtree level 1
2024-11-20 20:24:06.928807 INFO::Adjusting the last 1 batches sequentially
2024-11-20 20:24:06.930424 INFO::Done
2024-11-20 20:24:06.931025 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:06.933357 INFO::ASW Batch was -0.0568034216586079 prior to batch effect correction and is now -0.0568034216586079 .
2024-11-20 20:24:06.93436 INFO::Total function execution time is 0.339314460754395 s and adjustment time is 0.0928261280059814 s ( 27.36 )
2024-11-20 20:24:06.946683 INFO::Formatting Data.
2024-11-20 20:24:06.947335 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:06.948156 INFO::Removing potential empty rows and columns
2024-11-20 20:24:06.949167 INFO::Found 0 missing values.
2024-11-20 20:24:06.950086 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.
2024-11-20 20:24:06.959789 INFO::Formatting Data.
2024-11-20 20:24:06.960397 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:06.961173 INFO::Removing potential empty rows and columns
2024-11-20 20:24:06.962118 INFO::Found 0 missing values.
2024-11-20 20:24:06.962956 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.
2024-11-20 20:24:06.977347 INFO::Formatting Data.
2024-11-20 20:24:06.977976 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:06.978784 INFO::Removing potential empty rows and columns
2024-11-20 20:24:06.979724 INFO::Found 0 missing values.
2024-11-20 20:24:06.980557 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.
2024-11-20 20:24:06.984558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:06.985065 INFO::Done
2024-11-20 20:24:06.985556 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:06.987376 INFO::Starting hierarchical adjustment
2024-11-20 20:24:06.988048 INFO::Found 2 batches.
2024-11-20 20:24:06.988561 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:06.989151 INFO::Using default BPPARAM
2024-11-20 20:24:06.989679 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:06.990565 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:07.011757 INFO::Done
2024-11-20 20:24:07.012433 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:07.014394 INFO::ASW Batch was -0.0539056194240554 prior to batch effect correction and is now -0.121551134714645 .
2024-11-20 20:24:07.015171 INFO::Total function execution time is 0.0378391742706299 s and adjustment time is 0.023831844329834 s ( 62.98 )
2024-11-20 20:24:07.017815 INFO::Formatting Data.
2024-11-20 20:24:07.018435 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:07.027082 INFO::Formatting Data.
2024-11-20 20:24:07.027712 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:07.028563 INFO::Removing potential empty rows and columns
2024-11-20 20:24:07.029577 INFO::Found 0 missing values.
2024-11-20 20:24:07.032427 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:07.03294 INFO::Done
2024-11-20 20:24:07.033473 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:07.035411 INFO::Starting hierarchical adjustment
2024-11-20 20:24:07.057763 INFO::Found 2 batches.
2024-11-20 20:24:07.058766 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:07.059355 INFO::Using default BPPARAM
2024-11-20 20:24:07.059837 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:07.060672 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:07.073586 INFO::Done
2024-11-20 20:24:07.074139 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:07.075913 INFO::ASW Batch was 0.0166855649797947 prior to batch effect correction and is now -0.125751707751354 .
2024-11-20 20:24:07.076615 INFO::Total function execution time is 0.049551248550415 s and adjustment time is 0.0170977115631104 s ( 34.51 )
2024-11-20 20:24:07.077571 INFO::Formatting Data.
2024-11-20 20:24:07.078119 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:07.078918 INFO::Removing potential empty rows and columns
2024-11-20 20:24:07.079849 INFO::Found 0 missing values.
2024-11-20 20:24:07.082498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:07.083059 INFO::Done
2024-11-20 20:24:07.083587 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:07.085532 INFO::Starting hierarchical adjustment
2024-11-20 20:24:07.086242 INFO::Found 2 batches.
2024-11-20 20:24:07.086738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:07.087286 INFO::Using default BPPARAM
2024-11-20 20:24:07.087754 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:07.088591 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:07.101621 INFO::Done
2024-11-20 20:24:07.10216 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:07.103932 INFO::ASW Batch was 0.0166855649797947 prior to batch effect correction and is now -0.125751707751354 .
2024-11-20 20:24:07.104627 INFO::Total function execution time is 0.0270583629608154 s and adjustment time is 0.0155491828918457 s ( 57.47 )
2024-11-20 20:24:09.659419 INFO::Formatting Data.
2024-11-20 20:24:09.660326 INFO::Recognized SummarizedExperiment
2024-11-20 20:24:09.660859 INFO::Typecasting input to dataframe.
2024-11-20 20:24:09.691149 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:09.692341 INFO::Removing potential empty rows and columns
2024-11-20 20:24:09.696026 INFO::Found 0 missing values.
2024-11-20 20:24:09.703158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:09.703719 INFO::Done
2024-11-20 20:24:09.704268 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:09.708015 INFO::Starting hierarchical adjustment
2024-11-20 20:24:09.708672 INFO::Found 2 batches.
2024-11-20 20:24:09.709139 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:09.710118 INFO::Using default BPPARAM
2024-11-20 20:24:09.710598 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:09.711465 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:09.769704 INFO::Done
2024-11-20 20:24:09.770406 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:09.773947 INFO::ASW Batch was -0.0105182736824615 prior to batch effect correction and is now -0.105347514750511 .
2024-11-20 20:24:09.774781 INFO::Total function execution time is 0.115807294845581 s and adjustment time is 0.0611486434936523 s ( 52.8 )
2024-11-20 20:24:09.79321 INFO::Formatting Data.
2024-11-20 20:24:09.793962 INFO::Recognized SummarizedExperiment
2024-11-20 20:24:09.794527 INFO::Typecasting input to dataframe.
2024-11-20 20:24:09.803961 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:09.805081 INFO::Removing potential empty rows and columns
2024-11-20 20:24:09.80898 INFO::Found 0 missing values.
2024-11-20 20:24:09.816135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:09.816737 INFO::Done
2024-11-20 20:24:09.817281 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:09.820788 INFO::Starting hierarchical adjustment
2024-11-20 20:24:09.821513 INFO::Found 2 batches.
2024-11-20 20:24:09.822037 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:09.822632 INFO::Using default BPPARAM
2024-11-20 20:24:09.823136 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:09.824081 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:09.848679 INFO::Done
2024-11-20 20:24:09.849348 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:09.852779 INFO::ASW Batch was 0.0148927509231348 prior to batch effect correction and is now 0.0148927509231348 .
2024-11-20 20:24:09.853588 INFO::Total function execution time is 0.0603737831115723 s and adjustment time is 0.0272972583770752 s ( 45.21 )
2024-11-20 20:24:09.871068 INFO::Formatting Data.
2024-11-20 20:24:09.871811 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:09.872674 INFO::Removing potential empty rows and columns
2024-11-20 20:24:09.873709 INFO::Found 0 missing values.
2024-11-20 20:24:09.876655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:09.877171 INFO::Done
2024-11-20 20:24:09.877672 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:09.879575 INFO::Starting hierarchical adjustment
2024-11-20 20:24:09.880252 INFO::Found 3 batches.
2024-11-20 20:24:09.880762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:09.881363 INFO::Using default BPPARAM
2024-11-20 20:24:09.881873 INFO::Processing subtree level 1
2024-11-20 20:24:10.00841 INFO::Adjusting the last 1 batches sequentially
2024-11-20 20:24:10.010045 INFO::Done
2024-11-20 20:24:10.010643 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:10.012929 INFO::ASW Batch was -0.0688325096787089 prior to batch effect correction and is now -0.172224801765774 .
2024-11-20 20:24:10.01382 INFO::Total function execution time is 0.142773866653442 s and adjustment time is 0.129926919937134 s ( 91 )
2024-11-20 20:24:10.027128 INFO::Skipping initial DF formatting
2024-11-20 20:24:10.027947 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:10.031718 INFO::Starting hierarchical adjustment
2024-11-20 20:24:10.032445 INFO::Found 5 batches.
2024-11-20 20:24:10.032971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:10.033597 INFO::Using default BPPARAM
2024-11-20 20:24:10.034128 INFO::Processing subtree level 1
2024-11-20 20:24:10.14731 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:10.148819 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:10.167927 INFO::Done
2024-11-20 20:24:10.168596 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:10.172611 INFO::ASW Batch was 0.503781391689457 prior to batch effect correction and is now 0.503781391689457 .
2024-11-20 20:24:10.17322 INFO::ASW Label was 0.361171346348518 prior to batch effect correction and is now 0.361171346348518 .
2024-11-20 20:24:10.174019 INFO::Total function execution time is 0.146938562393188 s and adjustment time is 0.135624647140503 s ( 92.3 )
2024-11-20 20:24:10.190926 INFO::Formatting Data.
2024-11-20 20:24:10.19167 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:10.19256 INFO::Removing potential empty rows and columns
2024-11-20 20:24:10.193522 INFO::Found 0 missing values.
2024-11-20 20:24:10.197619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:10.198138 INFO::Done
2024-11-20 20:24:10.198658 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:10.201463 INFO::Starting hierarchical adjustment
2024-11-20 20:24:10.202157 INFO::Found 5 batches.
2024-11-20 20:24:10.202686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:10.203326 INFO::Using default BPPARAM
2024-11-20 20:24:10.203844 INFO::Processing subtree level 1
2024-11-20 20:24:10.302384 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:10.303854 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:10.318693 INFO::Done
2024-11-20 20:24:10.319339 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:10.322279 INFO::ASW Batch was 0.347099533590629 prior to batch effect correction and is now -0.0133803558939542 .
2024-11-20 20:24:10.322862 INFO::ASW Label was 0.418008456393737 prior to batch effect correction and is now 0.763528497485888 .
2024-11-20 20:24:10.323625 INFO::Total function execution time is 0.132752895355225 s and adjustment time is 0.116663455963135 s ( 87.88 )
2024-11-20 20:24:10.32441 INFO::Formatting Data.
2024-11-20 20:24:10.324998 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:10.325845 INFO::Removing potential empty rows and columns
2024-11-20 20:24:10.326799 INFO::Found 0 missing values.
2024-11-20 20:24:10.330859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:10.331396 INFO::Done
2024-11-20 20:24:10.331898 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:10.334593 INFO::Starting hierarchical adjustment
2024-11-20 20:24:10.335282 INFO::Found 5 batches.
2024-11-20 20:24:10.33579 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:10.336408 INFO::Using default BPPARAM
2024-11-20 20:24:10.33692 INFO::Processing subtree level 1
2024-11-20 20:24:10.436297 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:10.437817 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:10.453326 INFO::Done
2024-11-20 20:24:10.453995 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:10.457128 INFO::ASW Batch was 0.347099533590629 prior to batch effect correction and is now -0.0133803558939542 .
2024-11-20 20:24:10.457752 INFO::ASW Label was 0.418008456393737 prior to batch effect correction and is now 0.763528497485888 .
2024-11-20 20:24:10.458564 INFO::Total function execution time is 0.134149312973022 s and adjustment time is 0.118152618408203 s ( 88.08 )
2024-11-20 20:24:10.472017 INFO::Formatting Data.
2024-11-20 20:24:10.472724 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:10.473628 INFO::Removing potential empty rows and columns
2024-11-20 20:24:10.47463 INFO::Found 0 missing values.
2024-11-20 20:24:10.478609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:10.479131 INFO::Done
2024-11-20 20:24:10.479652 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:10.482424 INFO::Starting hierarchical adjustment
2024-11-20 20:24:10.483124 INFO::Found 5 batches.
2024-11-20 20:24:10.483656 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:10.484288 INFO::Using default BPPARAM
2024-11-20 20:24:10.484809 INFO::Processing subtree level 1
2024-11-20 20:24:10.58573 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:10.587247 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:10.602238 INFO::Done
2024-11-20 20:24:10.602904 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:10.605975 INFO::ASW Batch was 0.388679773266649 prior to batch effect correction and is now -0.108180657862396 .
2024-11-20 20:24:10.606571 INFO::ASW Label was 0.378638458271141 prior to batch effect correction and is now 0.875192930306331 .
2024-11-20 20:24:10.607373 INFO::Total function execution time is 0.135358810424805 s and adjustment time is 0.119234085083008 s ( 88.09 )
2024-11-20 20:24:10.608187 INFO::Formatting Data.
2024-11-20 20:24:10.608826 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:10.609706 INFO::Removing potential empty rows and columns
2024-11-20 20:24:10.610685 INFO::Found 0 missing values.
2024-11-20 20:24:10.621831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:10.62249 INFO::Done
2024-11-20 20:24:10.623049 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:10.62618 INFO::Starting hierarchical adjustment
2024-11-20 20:24:10.626907 INFO::Found 5 batches.
2024-11-20 20:24:10.627433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:10.628078 INFO::Using default BPPARAM
2024-11-20 20:24:10.628606 INFO::Processing subtree level 1
2024-11-20 20:24:10.730054 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:10.731657 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:10.746811 INFO::Done
2024-11-20 20:24:10.74747 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:10.750431 INFO::ASW Batch was 0.388679773266649 prior to batch effect correction and is now -0.108180657862396 .
2024-11-20 20:24:10.751016 INFO::ASW Label was 0.378638458271141 prior to batch effect correction and is now 0.875192930306331 .
2024-11-20 20:24:10.751812 INFO::Total function execution time is 0.143603801727295 s and adjustment time is 0.120059967041016 s ( 83.61 )
2024-11-20 20:24:10.764764 INFO::Formatting Data.
2024-11-20 20:24:10.765457 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:10.766349 INFO::Removing potential empty rows and columns
2024-11-20 20:24:10.767376 INFO::Found 0 missing values.
2024-11-20 20:24:10.770014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:10.770539 INFO::Done
2024-11-20 20:24:10.771051 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:10.773798 INFO::Starting hierarchical adjustment
2024-11-20 20:24:10.774487 INFO::Found 2 batches.
2024-11-20 20:24:10.775001 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:10.775632 INFO::Using default BPPARAM
2024-11-20 20:24:10.776159 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:10.777029 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:10.846792 INFO::Done
2024-11-20 20:24:10.848156 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:10.850841 INFO::ASW Batch was 0.56738355272915 prior to batch effect correction and is now 0.0265357883646544 .
2024-11-20 20:24:10.851403 INFO::ASW Label was 0.533579059081369 prior to batch effect correction and is now 0.887243130524566 .
2024-11-20 20:24:10.852173 INFO::Total function execution time is 0.0874514579772949 s and adjustment time is 0.0724136829376221 s ( 82.8 )
2024-11-20 20:24:10.852949 INFO::Formatting Data.
2024-11-20 20:24:10.853563 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:10.854418 INFO::Removing potential empty rows and columns
2024-11-20 20:24:10.855369 INFO::Found 0 missing values.
2024-11-20 20:24:10.857938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:10.858473 INFO::Done
2024-11-20 20:24:10.858979 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:10.861705 INFO::Starting hierarchical adjustment
2024-11-20 20:24:10.862461 INFO::Found 2 batches.
2024-11-20 20:24:10.863096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:10.863751 INFO::Using default BPPARAM
2024-11-20 20:24:10.864308 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:10.865246 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:10.879899 INFO::Done
2024-11-20 20:24:10.880466 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:10.883041 INFO::ASW Batch was 0.56738355272915 prior to batch effect correction and is now 0.0265357883646544 .
2024-11-20 20:24:10.883588 INFO::ASW Label was 0.533579059081369 prior to batch effect correction and is now 0.887243130524566 .
2024-11-20 20:24:10.884317 INFO::Total function execution time is 0.0313899517059326 s and adjustment time is 0.0176224708557129 s ( 56.14 )
2024-11-20 20:24:10.894557 INFO::Formatting Data.
2024-11-20 20:24:10.895144 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:10.895962 INFO::Removing potential empty rows and columns
2024-11-20 20:24:10.896797 INFO::Found 0 missing values.
2024-11-20 20:24:10.89873 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:10.899251 INFO::Done
2024-11-20 20:24:10.899751 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:10.901389 INFO::Starting hierarchical adjustment
2024-11-20 20:24:10.902038 INFO::Found 2 batches.
2024-11-20 20:24:10.90255 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:10.903113 INFO::Using default BPPARAM
2024-11-20 20:24:10.903608 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:10.904463 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:10.933636 INFO::Done
2024-11-20 20:24:10.934292 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:10.936132 INFO::ASW Batch was 0.196732420381269 prior to batch effect correction and is now -0.0338175088006895 .
2024-11-20 20:24:10.93692 INFO::Total function execution time is 0.0423920154571533 s and adjustment time is 0.0317180156707764 s ( 74.82 )
2024-11-20 20:24:10.948182 INFO::Formatting Data.
2024-11-20 20:24:10.948865 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:10.949708 INFO::Removing potential empty rows and columns
2024-11-20 20:24:10.950705 INFO::Found 0 missing values.
2024-11-20 20:24:10.951791 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.
2024-11-20 20:24:10.956253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:10.956908 INFO::Done
2024-11-20 20:24:10.957431 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:10.960152 INFO::Starting hierarchical adjustment
2024-11-20 20:24:10.960828 INFO::Found 2 batches.
2024-11-20 20:24:10.96133 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:10.961922 INFO::Using default BPPARAM
2024-11-20 20:24:10.962432 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:10.963337 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:10.979665 INFO::Done
2024-11-20 20:24:10.980262 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:10.982971 INFO::ASW Batch was 0.416419837628562 prior to batch effect correction and is now 0.0465929605481397 .
2024-11-20 20:24:10.983515 INFO::ASW Label was 0.67741847008082 prior to batch effect correction and is now 0.900178484802299 .
2024-11-20 20:24:10.98427 INFO::Total function execution time is 0.0361261367797852 s and adjustment time is 0.0189721584320068 s ( 52.52 )
2024-11-20 20:24:10.985 INFO::Formatting Data.
2024-11-20 20:24:10.985594 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:10.986471 INFO::Removing potential empty rows and columns
2024-11-20 20:24:10.987385 INFO::Found 0 missing values.
2024-11-20 20:24:10.988229 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.
2024-11-20 20:24:10.992413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:10.992929 INFO::Done
2024-11-20 20:24:10.993431 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:10.996052 INFO::Starting hierarchical adjustment
2024-11-20 20:24:10.99674 INFO::Found 2 batches.
2024-11-20 20:24:10.997254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:10.997844 INFO::Using default BPPARAM
2024-11-20 20:24:10.998369 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:10.999278 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:11.015271 INFO::Done
2024-11-20 20:24:11.015858 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:11.018663 INFO::ASW Batch was 0.416419837628562 prior to batch effect correction and is now 0.0465929605481397 .
2024-11-20 20:24:11.019235 INFO::ASW Label was 0.67741847008082 prior to batch effect correction and is now 0.900178484802299 .
2024-11-20 20:24:11.020022 INFO::Total function execution time is 0.0350139141082764 s and adjustment time is 0.0186638832092285 s ( 53.3 )
2024-11-20 20:24:11.199344 INFO::Formatting Data.
2024-11-20 20:24:11.200062 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:11.200859 INFO::Removing potential empty rows and columns
2024-11-20 20:24:11.201796 INFO::Found 0 missing values.
2024-11-20 20:24:11.204499 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:11.204995 INFO::Done
2024-11-20 20:24:11.205475 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:11.207279 INFO::Starting hierarchical adjustment
2024-11-20 20:24:11.207929 INFO::Found 3 batches.
2024-11-20 20:24:11.20842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:11.208991 INFO::Using default BPPARAM
2024-11-20 20:24:11.209481 INFO::Processing subtree level 1
2024-11-20 20:24:11.297511 INFO::Adjusting the last 1 batches sequentially
2024-11-20 20:24:11.299158 INFO::Done
2024-11-20 20:24:11.299782 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:11.302045 INFO::ASW Batch was 0.0684009704588576 prior to batch effect correction and is now 0.0684009704588576 .
2024-11-20 20:24:11.302933 INFO::Total function execution time is 0.103621959686279 s and adjustment time is 0.0913417339324951 s ( 88.15 )
2024-11-20 20:24:11.30398 INFO::Formatting Data.
2024-11-20 20:24:11.30462 INFO::Typecasting input to dataframe.
2024-11-20 20:24:11.305339 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:11.306208 INFO::Removing potential empty rows and columns
2024-11-20 20:24:11.307239 INFO::Found 0 missing values.
2024-11-20 20:24:11.310052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:11.31057 INFO::Done
2024-11-20 20:24:11.311111 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:11.312983 INFO::Starting hierarchical adjustment
2024-11-20 20:24:11.313686 INFO::Found 3 batches.
2024-11-20 20:24:11.314189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:11.31478 INFO::Using default BPPARAM
2024-11-20 20:24:11.315285 INFO::Processing subtree level 1
2024-11-20 20:24:11.400437 INFO::Adjusting the last 1 batches sequentially
2024-11-20 20:24:11.40213 INFO::Done
2024-11-20 20:24:11.40275 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:11.405007 INFO::ASW Batch was 0.0684009704588576 prior to batch effect correction and is now 0.0684009704588576 .
2024-11-20 20:24:11.405887 INFO::Total function execution time is 0.101899385452271 s and adjustment time is 0.0885591506958008 s ( 86.91 )
2024-11-20 20:24:11.417543 INFO::Formatting Data.
2024-11-20 20:24:11.418206 INFO::Typecasting input to dataframe.
2024-11-20 20:24:11.41899 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:11.419822 INFO::Removing potential empty rows and columns
2024-11-20 20:24:11.420822 INFO::Found 0 missing values.
2024-11-20 20:24:11.423523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:11.424036 INFO::Done
2024-11-20 20:24:11.424538 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:11.426339 INFO::Starting hierarchical adjustment
2024-11-20 20:24:11.427025 INFO::Found 3 batches.
2024-11-20 20:24:11.427547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:11.428124 INFO::Using default BPPARAM
2024-11-20 20:24:11.428638 INFO::Processing subtree level 1
2024-11-20 20:24:11.511851 INFO::Adjusting the last 1 batches sequentially
2024-11-20 20:24:11.513486 INFO::Done
2024-11-20 20:24:11.514073 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:11.516363 INFO::ASW Batch was -0.106650500286551 prior to batch effect correction and is now -0.106650500286551 .
2024-11-20 20:24:11.517229 INFO::Total function execution time is 0.0996911525726318 s and adjustment time is 0.086578369140625 s ( 86.85 )
2024-11-20 20:24:11.646518 INFO::Formatting Data.
2024-11-20 20:24:11.64721 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:11.648222 INFO::Removing potential empty rows and columns
2024-11-20 20:24:11.650736 INFO::Found 1000 missing values.
2024-11-20 20:24:11.675407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:11.6761 INFO::Done
2024-11-20 20:24:11.676668 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:11.682103 INFO::Starting hierarchical adjustment
2024-11-20 20:24:11.682848 INFO::Found 10 batches.
2024-11-20 20:24:11.683403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:11.684071 INFO::Using default BPPARAM
2024-11-20 20:24:11.684638 INFO::Processing subtree level 1
2024-11-20 20:24:11.840744 INFO::Processing subtree level 2
2024-11-20 20:24:11.997081 INFO::Adjusting the last 1 batches sequentially
2024-11-20 20:24:11.999522 INFO::Done
2024-11-20 20:24:12.000356 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:12.007414 INFO::ASW Batch was 0.50236949309426 prior to batch effect correction and is now 0.50236949309426 .
2024-11-20 20:24:12.00832 INFO::ASW Label was 0.312308316786263 prior to batch effect correction and is now 0.312308316786263 .
2024-11-20 20:24:12.009482 INFO::Total function execution time is 0.362928152084351 s and adjustment time is 0.316775321960449 s ( 87.28 )
2024-11-20 20:24:12.010604 INFO::Formatting Data.
2024-11-20 20:24:12.011475 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:12.013063 INFO::Removing potential empty rows and columns
2024-11-20 20:24:12.016769 INFO::Found 1000 missing values.
2024-11-20 20:24:12.042697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:12.043555 INFO::Done
2024-11-20 20:24:12.044258 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:12.050582 INFO::Starting hierarchical adjustment
2024-11-20 20:24:12.051442 INFO::Found 10 batches.
2024-11-20 20:24:12.953185 INFO::Set up parallel execution backend with 2 workers
2024-11-20 20:24:12.954907 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-11-20 20:24:13.955811 INFO::Adjusting the last 2 batches sequentially
2024-11-20 20:24:13.958379 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 20:24:13.977932 INFO::Done
2024-11-20 20:24:13.978586 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:13.983522 INFO::ASW Batch was 0.50236949309426 prior to batch effect correction and is now 0.50236949309426 .
2024-11-20 20:24:13.984085 INFO::ASW Label was 0.312308316786263 prior to batch effect correction and is now 0.312308316786263 .
2024-11-20 20:24:13.984902 INFO::Total function execution time is 1.97437810897827 s and adjustment time is 1.92667818069458 s ( 97.58 )
2024-11-20 20:24:14.137865 INFO::Formatting Data.
2024-11-20 20:24:14.138652 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.139616 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.140695 INFO::Found 0 missing values.
2024-11-20 20:24:14.144366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.144949 INFO::Done
2024-11-20 20:24:14.145497 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 20:24:14.148286 INFO::Starting hierarchical adjustment
2024-11-20 20:24:14.148996 INFO::Found 3 batches.
2024-11-20 20:24:14.149555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 20:24:14.150183 INFO::Using default BPPARAM
2024-11-20 20:24:14.150731 INFO::Processing subtree level 1
2024-11-20 20:24:14.254642 INFO::Adjusting the last 1 batches sequentially
2024-11-20 20:24:14.256454 INFO::Done
2024-11-20 20:24:14.257071 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 20:24:14.260263 INFO::ASW Batch was 0.2112464163439 prior to batch effect correction and is now -0.159236323111603 .
2024-11-20 20:24:14.260875 INFO::ASW Label was -0.164282691303211 prior to batch effect correction and is now 0.0812003306940673 .
2024-11-20 20:24:14.261809 INFO::Total function execution time is 0.123975276947021 s and adjustment time is 0.107589721679688 s ( 86.78 )
2024-11-20 20:24:14.36915 INFO::Formatting Data.
2024-11-20 20:24:14.369891 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.370739 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.371736 INFO::Found 2 missing values.
2024-11-20 20:24:14.374406 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.374918 INFO::Done
2024-11-20 20:24:14.399906 INFO::Found NA in Reference column
2024-11-20 20:24:14.408287 INFO::Require at least two references per batch.
2024-11-20 20:24:14.426042 INFO::Formatting Data.
2024-11-20 20:24:14.426673 INFO::Recognized SummarizedExperiment
2024-11-20 20:24:14.427172 INFO::Typecasting input to dataframe.
2024-11-20 20:24:14.43575 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.436757 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.440066 INFO::Found 0 missing values.
2024-11-20 20:24:14.446365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.446868 INFO::Done
2024-11-20 20:24:14.459898 INFO::Formatting Data.
2024-11-20 20:24:14.460473 INFO::Recognized SummarizedExperiment
2024-11-20 20:24:14.460964 INFO::Typecasting input to dataframe.
2024-11-20 20:24:14.476485 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.477585 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.480954 INFO::Found 0 missing values.
2024-11-20 20:24:14.491349 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.491974 INFO::Done
2024-11-20 20:24:14.50547 INFO::Formatting Data.
2024-11-20 20:24:14.506149 INFO::Recognized SummarizedExperiment
2024-11-20 20:24:14.506662 INFO::Typecasting input to dataframe.
2024-11-20 20:24:14.521555 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.522515 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.52353 INFO::Found 0 missing values.
2024-11-20 20:24:14.524434 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.
2024-11-20 20:24:14.528508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.529019 INFO::Done
2024-11-20 20:24:14.537946 INFO::Formatting Data.
2024-11-20 20:24:14.538577 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.539361 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.540304 INFO::Found 0 missing values.
2024-11-20 20:24:14.542908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.543411 INFO::Done
2024-11-20 20:24:14.553257 INFO::Formatting Data.
2024-11-20 20:24:14.55389 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.554671 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.555576 INFO::Found 0 missing values.
2024-11-20 20:24:14.55818 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.558719 INFO::Done
2024-11-20 20:24:14.584884 INFO::Formatting Data.
2024-11-20 20:24:14.585615 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.586591 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.587689 INFO::Found 1 missing values.
2024-11-20 20:24:14.590099 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.590604 INFO::Done
2024-11-20 20:24:14.607251 INFO::Formatting Data.
2024-11-20 20:24:14.607946 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.608739 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.609622 INFO::Found 2 missing values.
2024-11-20 20:24:14.610467 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.
2024-11-20 20:24:14.612642 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.613213 INFO::Done
2024-11-20 20:24:14.622152 INFO::Formatting Data.
2024-11-20 20:24:14.622803 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.623608 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.624452 INFO::Found 2 missing values.
2024-11-20 20:24:14.625905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.626403 INFO::Done
2024-11-20 20:24:14.63559 INFO::Formatting Data.
2024-11-20 20:24:14.636273 INFO::Typecasting input to dataframe.
2024-11-20 20:24:14.637012 INFO::Replacing NaNs with NAs.
2024-11-20 20:24:14.637807 INFO::Removing potential empty rows and columns
2024-11-20 20:24:14.638744 INFO::Found 0 missing values.
2024-11-20 20:24:14.641388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 20:24:14.641883 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 138 ]
>
> proc.time()
user system elapsed
14.907 3.211 17.870
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 20.506 | 1.070 | 14.713 | |
| compute_asw | 0.022 | 0.000 | 0.023 | |
| count_existing | 0.012 | 0.001 | 0.013 | |
| generate_data_covariables | 0.010 | 0.001 | 0.011 | |
| generate_dataset | 0.010 | 0.000 | 0.011 | |