Yannis Schumann
| Snapshot Date: 2024-05-15 14:05:05 -0400 (Wed, 15 May 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-17 11:36:26 -0400 (Fri, 17 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4663 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4398 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4425 |
| 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 154/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.1.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.0.tar.gz |
| StartedAt: 2024-05-15 20:23:00 -0400 (Wed, 15 May 2024) |
| EndedAt: 2024-05-15 20:24:28 -0400 (Wed, 15 May 2024) |
| EllapsedTime: 88.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.623 1.299 17.765
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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")
2024-05-15 20:23:52.437789 INFO::Formatting Data.
2024-05-15 20:23:52.439331 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:52.450257 INFO::Removing potential empty rows and columns
2024-05-15 20:23:52.716245 INFO::Found 0 missing values.
2024-05-15 20:23:52.719827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:52.720545 INFO::Done
2024-05-15 20:23:52.721092 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:52.733463 INFO::Starting hierarchical adjustment
2024-05-15 20:23:52.734393 INFO::Found 3 batches.
2024-05-15 20:23:52.734959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:52.736126 INFO::Using default BPPARAM
2024-05-15 20:23:52.736718 INFO::Processing subtree level 1
2024-05-15 20:23:52.833014 INFO::Adjusting the last 1 batches sequentially
2024-05-15 20:23:52.834948 INFO::Done
2024-05-15 20:23:52.835654 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:52.838369 INFO::ASW Batch was -0.0714956381731224 prior to batch effect correction and is now -0.0714956381731224 .
2024-05-15 20:23:52.839521 INFO::Total function execution time is 0.402609825134277 s and adjustment time is 0.100740671157837 s ( 25.02 )
2024-05-15 20:23:52.859761 INFO::Formatting Data.
2024-05-15 20:23:52.860733 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:52.861882 INFO::Removing potential empty rows and columns
2024-05-15 20:23:52.863065 INFO::Found 0 missing values.
2024-05-15 20:23:52.864092 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.
2024-05-15 20:23:52.876212 INFO::Formatting Data.
2024-05-15 20:23:52.876992 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:52.877964 INFO::Removing potential empty rows and columns
2024-05-15 20:23:52.879032 INFO::Found 0 missing values.
2024-05-15 20:23:52.879989 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.
2024-05-15 20:23:52.896311 INFO::Formatting Data.
2024-05-15 20:23:52.897136 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:52.898066 INFO::Removing potential empty rows and columns
2024-05-15 20:23:52.899085 INFO::Found 0 missing values.
2024-05-15 20:23:52.899972 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.
2024-05-15 20:23:52.90434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:52.904864 INFO::Done
2024-05-15 20:23:52.905434 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:52.907705 INFO::Starting hierarchical adjustment
2024-05-15 20:23:52.90838 INFO::Found 2 batches.
2024-05-15 20:23:52.908874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:52.909519 INFO::Using default BPPARAM
2024-05-15 20:23:52.910028 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:52.910932 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:52.933913 INFO::Done
2024-05-15 20:23:52.934603 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:52.936636 INFO::ASW Batch was 0.106682188972028 prior to batch effect correction and is now -0.125435475778152 .
2024-05-15 20:23:52.937442 INFO::Total function execution time is 0.041201114654541 s and adjustment time is 0.0256311893463135 s ( 62.21 )
2024-05-15 20:23:52.940305 INFO::Formatting Data.
2024-05-15 20:23:52.940915 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:52.949617 INFO::Formatting Data.
2024-05-15 20:23:52.950301 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:52.951133 INFO::Removing potential empty rows and columns
2024-05-15 20:23:52.952107 INFO::Found 0 missing values.
2024-05-15 20:23:52.954804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:52.955299 INFO::Done
2024-05-15 20:23:52.955771 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:52.957713 INFO::Starting hierarchical adjustment
2024-05-15 20:23:52.958374 INFO::Found 2 batches.
2024-05-15 20:23:52.958853 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:52.959408 INFO::Using default BPPARAM
2024-05-15 20:23:52.959868 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:52.960717 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:52.975004 INFO::Done
2024-05-15 20:23:52.975595 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:52.977537 INFO::ASW Batch was -0.0105296138902825 prior to batch effect correction and is now -0.112370383566164 .
2024-05-15 20:23:52.978276 INFO::Total function execution time is 0.0287232398986816 s and adjustment time is 0.0167694091796875 s ( 58.38 )
2024-05-15 20:23:52.979292 INFO::Formatting Data.
2024-05-15 20:23:52.979859 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:52.980672 INFO::Removing potential empty rows and columns
2024-05-15 20:23:52.981665 INFO::Found 0 missing values.
2024-05-15 20:23:52.984325 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:52.984815 INFO::Done
2024-05-15 20:23:52.98531 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:52.987216 INFO::Starting hierarchical adjustment
2024-05-15 20:23:52.987856 INFO::Found 2 batches.
2024-05-15 20:23:52.988345 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:52.988891 INFO::Using default BPPARAM
2024-05-15 20:23:52.989391 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:52.990219 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:53.004574 INFO::Done
2024-05-15 20:23:53.005219 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:53.007142 INFO::ASW Batch was -0.0105296138902825 prior to batch effect correction and is now -0.112370383566164 .
2024-05-15 20:23:53.007871 INFO::Total function execution time is 0.0285854339599609 s and adjustment time is 0.0168294906616211 s ( 58.87 )
2024-05-15 20:23:55.171299 INFO::Formatting Data.
2024-05-15 20:23:55.172015 INFO::Recognized SummarizedExperiment
2024-05-15 20:23:55.172466 INFO::Typecasting input to dataframe.
2024-05-15 20:23:55.202121 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:55.203251 INFO::Removing potential empty rows and columns
2024-05-15 20:23:55.206409 INFO::Found 0 missing values.
2024-05-15 20:23:55.212033 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:55.212524 INFO::Done
2024-05-15 20:23:55.212958 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:55.216026 INFO::Starting hierarchical adjustment
2024-05-15 20:23:55.216635 INFO::Found 2 batches.
2024-05-15 20:23:55.217085 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:55.218031 INFO::Using default BPPARAM
2024-05-15 20:23:55.218476 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:55.219299 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:55.309199 INFO::Done
2024-05-15 20:23:55.309844 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:55.312756 INFO::ASW Batch was -0.00805697974239224 prior to batch effect correction and is now -0.0934496797100938 .
2024-05-15 20:23:55.313507 INFO::Total function execution time is 0.142547845840454 s and adjustment time is 0.0926582813262939 s ( 65 )
2024-05-15 20:23:55.328914 INFO::Formatting Data.
2024-05-15 20:23:55.329562 INFO::Recognized SummarizedExperiment
2024-05-15 20:23:55.330005 INFO::Typecasting input to dataframe.
2024-05-15 20:23:55.33787 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:55.338876 INFO::Removing potential empty rows and columns
2024-05-15 20:23:55.341719 INFO::Found 0 missing values.
2024-05-15 20:23:55.347334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:55.347822 INFO::Done
2024-05-15 20:23:55.34827 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:55.351167 INFO::Starting hierarchical adjustment
2024-05-15 20:23:55.351776 INFO::Found 2 batches.
2024-05-15 20:23:55.352213 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:55.352712 INFO::Using default BPPARAM
2024-05-15 20:23:55.353141 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:55.354028 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:55.373962 INFO::Done
2024-05-15 20:23:55.37455 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:55.377403 INFO::ASW Batch was -0.00189472116474883 prior to batch effect correction and is now -0.00189472116474883 .
2024-05-15 20:23:55.378127 INFO::Total function execution time is 0.0492029190063477 s and adjustment time is 0.0222911834716797 s ( 45.3 )
2024-05-15 20:23:55.392474 INFO::Formatting Data.
2024-05-15 20:23:55.393093 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:55.393857 INFO::Removing potential empty rows and columns
2024-05-15 20:23:55.394732 INFO::Found 0 missing values.
2024-05-15 20:23:55.39703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:55.397494 INFO::Done
2024-05-15 20:23:55.39794 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:55.399586 INFO::Starting hierarchical adjustment
2024-05-15 20:23:55.400155 INFO::Found 3 batches.
2024-05-15 20:23:55.400578 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:55.401058 INFO::Using default BPPARAM
2024-05-15 20:23:55.401495 INFO::Processing subtree level 1
2024-05-15 20:23:55.571989 INFO::Adjusting the last 1 batches sequentially
2024-05-15 20:23:55.573926 INFO::Done
2024-05-15 20:23:55.574592 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:55.577284 INFO::ASW Batch was -0.0510178717740372 prior to batch effect correction and is now -0.148820940590236 .
2024-05-15 20:23:55.578331 INFO::Total function execution time is 0.185807228088379 s and adjustment time is 0.173848152160645 s ( 93.56 )
2024-05-15 20:23:55.594615 INFO::Skipping initial DF formatting
2024-05-15 20:23:55.595318 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:55.599663 INFO::Starting hierarchical adjustment
2024-05-15 20:23:55.60043 INFO::Found 5 batches.
2024-05-15 20:23:55.600968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:55.601619 INFO::Using default BPPARAM
2024-05-15 20:23:55.602173 INFO::Processing subtree level 1
2024-05-15 20:23:55.744548 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:55.746122 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:55.766841 INFO::Done
2024-05-15 20:23:55.767482 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:55.771621 INFO::ASW Batch was 0.5150490571906 prior to batch effect correction and is now 0.5150490571906 .
2024-05-15 20:23:55.772255 INFO::ASW Label was 0.352319817765837 prior to batch effect correction and is now 0.352319817765837 .
2024-05-15 20:23:55.773246 INFO::Total function execution time is 0.178695440292358 s and adjustment time is 0.166570663452148 s ( 93.21 )
2024-05-15 20:23:55.789743 INFO::Formatting Data.
2024-05-15 20:23:55.790493 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:55.791361 INFO::Removing potential empty rows and columns
2024-05-15 20:23:55.792297 INFO::Found 0 missing values.
2024-05-15 20:23:55.795983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:55.796482 INFO::Done
2024-05-15 20:23:55.796979 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:55.799773 INFO::Starting hierarchical adjustment
2024-05-15 20:23:55.80043 INFO::Found 5 batches.
2024-05-15 20:23:55.8009 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:55.80148 INFO::Using default BPPARAM
2024-05-15 20:23:55.801951 INFO::Processing subtree level 1
2024-05-15 20:23:55.943594 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:55.946287 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:55.966902 INFO::Done
2024-05-15 20:23:55.968285 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:55.9722 INFO::ASW Batch was 0.252772745770931 prior to batch effect correction and is now -0.108366604603407 .
2024-05-15 20:23:55.972874 INFO::ASW Label was 0.391898966656498 prior to batch effect correction and is now 0.902366165550265 .
2024-05-15 20:23:55.973788 INFO::Total function execution time is 0.184080839157104 s and adjustment time is 0.166501998901367 s ( 90.45 )
2024-05-15 20:23:55.974679 INFO::Formatting Data.
2024-05-15 20:23:55.975287 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:55.976234 INFO::Removing potential empty rows and columns
2024-05-15 20:23:55.977333 INFO::Found 0 missing values.
2024-05-15 20:23:55.981482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:55.982025 INFO::Done
2024-05-15 20:23:55.98254 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:55.98562 INFO::Starting hierarchical adjustment
2024-05-15 20:23:55.986349 INFO::Found 5 batches.
2024-05-15 20:23:55.986867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:55.987487 INFO::Using default BPPARAM
2024-05-15 20:23:55.987997 INFO::Processing subtree level 1
2024-05-15 20:23:56.108562 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:56.110363 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:56.128475 INFO::Done
2024-05-15 20:23:56.129428 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:56.133016 INFO::ASW Batch was 0.252772745770931 prior to batch effect correction and is now -0.108366604603407 .
2024-05-15 20:23:56.1337 INFO::ASW Label was 0.391898966656498 prior to batch effect correction and is now 0.902366165550265 .
2024-05-15 20:23:56.134633 INFO::Total function execution time is 0.159933567047119 s and adjustment time is 0.142229557037354 s ( 88.93 )
2024-05-15 20:23:56.14902 INFO::Formatting Data.
2024-05-15 20:23:56.149911 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:56.150874 INFO::Removing potential empty rows and columns
2024-05-15 20:23:56.151904 INFO::Found 0 missing values.
2024-05-15 20:23:56.156194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:56.156759 INFO::Done
2024-05-15 20:23:56.157323 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:56.16049 INFO::Starting hierarchical adjustment
2024-05-15 20:23:56.161262 INFO::Found 5 batches.
2024-05-15 20:23:56.161794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:56.162426 INFO::Using default BPPARAM
2024-05-15 20:23:56.162975 INFO::Processing subtree level 1
2024-05-15 20:23:56.288635 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:56.290498 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:56.307839 INFO::Done
2024-05-15 20:23:56.308627 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:56.312143 INFO::ASW Batch was 0.308900780927276 prior to batch effect correction and is now -0.0807965796115634 .
2024-05-15 20:23:56.312846 INFO::ASW Label was 0.422593115946394 prior to batch effect correction and is now 0.851271541588925 .
2024-05-15 20:23:56.313754 INFO::Total function execution time is 0.164775133132935 s and adjustment time is 0.146724462509155 s ( 89.05 )
2024-05-15 20:23:56.314667 INFO::Formatting Data.
2024-05-15 20:23:56.315305 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:56.316254 INFO::Removing potential empty rows and columns
2024-05-15 20:23:56.317289 INFO::Found 0 missing values.
2024-05-15 20:23:56.321551 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:56.322091 INFO::Done
2024-05-15 20:23:56.322613 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:56.325739 INFO::Starting hierarchical adjustment
2024-05-15 20:23:56.32645 INFO::Found 5 batches.
2024-05-15 20:23:56.326967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:56.327576 INFO::Using default BPPARAM
2024-05-15 20:23:56.328094 INFO::Processing subtree level 1
2024-05-15 20:23:56.451956 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:56.4536 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:56.468739 INFO::Done
2024-05-15 20:23:56.472184 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:56.476498 INFO::ASW Batch was 0.308900780927276 prior to batch effect correction and is now -0.0807965796115634 .
2024-05-15 20:23:56.47756 INFO::ASW Label was 0.422593115946394 prior to batch effect correction and is now 0.851271541588925 .
2024-05-15 20:23:56.478872 INFO::Total function execution time is 0.164164781570435 s and adjustment time is 0.14240837097168 s ( 86.75 )
2024-05-15 20:23:56.493979 INFO::Formatting Data.
2024-05-15 20:23:56.494751 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:56.495726 INFO::Removing potential empty rows and columns
2024-05-15 20:23:56.496823 INFO::Found 0 missing values.
2024-05-15 20:23:56.499655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:56.500201 INFO::Done
2024-05-15 20:23:56.500751 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:56.503935 INFO::Starting hierarchical adjustment
2024-05-15 20:23:56.504654 INFO::Found 2 batches.
2024-05-15 20:23:56.505204 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:56.505857 INFO::Using default BPPARAM
2024-05-15 20:23:56.506405 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:56.507337 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:56.523087 INFO::Done
2024-05-15 20:23:56.523695 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:56.526543 INFO::ASW Batch was 0.66516982785387 prior to batch effect correction and is now 0.0912532478883907 .
2024-05-15 20:23:56.527121 INFO::ASW Label was 0.455096377142656 prior to batch effect correction and is now 0.8563786466722 .
2024-05-15 20:23:56.527885 INFO::Total function execution time is 0.0340166091918945 s and adjustment time is 0.0185859203338623 s ( 54.64 )
2024-05-15 20:23:56.528652 INFO::Formatting Data.
2024-05-15 20:23:56.529243 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:56.53006 INFO::Removing potential empty rows and columns
2024-05-15 20:23:56.530976 INFO::Found 0 missing values.
2024-05-15 20:23:56.533511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:56.534009 INFO::Done
2024-05-15 20:23:56.534488 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:56.537344 INFO::Starting hierarchical adjustment
2024-05-15 20:23:56.53805 INFO::Found 2 batches.
2024-05-15 20:23:56.538547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:56.53913 INFO::Using default BPPARAM
2024-05-15 20:23:56.539633 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:56.540534 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:56.555384 INFO::Done
2024-05-15 20:23:56.555999 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:56.558872 INFO::ASW Batch was 0.66516982785387 prior to batch effect correction and is now 0.0912532478883907 .
2024-05-15 20:23:56.559424 INFO::ASW Label was 0.455096377142656 prior to batch effect correction and is now 0.8563786466722 .
2024-05-15 20:23:56.560155 INFO::Total function execution time is 0.0315182209014893 s and adjustment time is 0.0174643993377686 s ( 55.41 )
2024-05-15 20:23:56.570816 INFO::Formatting Data.
2024-05-15 20:23:56.571509 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:56.572356 INFO::Removing potential empty rows and columns
2024-05-15 20:23:56.573236 INFO::Found 0 missing values.
2024-05-15 20:23:56.575231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:56.575728 INFO::Done
2024-05-15 20:23:56.576209 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:56.578125 INFO::Starting hierarchical adjustment
2024-05-15 20:23:56.57881 INFO::Found 2 batches.
2024-05-15 20:23:56.579308 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:56.579892 INFO::Using default BPPARAM
2024-05-15 20:23:56.580416 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:56.581298 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:56.613355 INFO::Done
2024-05-15 20:23:56.614064 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:56.616123 INFO::ASW Batch was -0.0708375665202607 prior to batch effect correction and is now -0.142197222021716 .
2024-05-15 20:23:56.616925 INFO::Total function execution time is 0.0461745262145996 s and adjustment time is 0.0346744060516357 s ( 75.09 )
2024-05-15 20:23:56.628709 INFO::Formatting Data.
2024-05-15 20:23:56.629493 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:56.630378 INFO::Removing potential empty rows and columns
2024-05-15 20:23:56.631361 INFO::Found 0 missing values.
2024-05-15 20:23:56.632548 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.
2024-05-15 20:23:56.659029 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:56.659904 INFO::Done
2024-05-15 20:23:56.660409 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:56.663553 INFO::Starting hierarchical adjustment
2024-05-15 20:23:56.66429 INFO::Found 2 batches.
2024-05-15 20:23:56.664823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:56.665436 INFO::Using default BPPARAM
2024-05-15 20:23:56.665942 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:56.66694 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:56.685081 INFO::Done
2024-05-15 20:23:56.685816 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:56.688879 INFO::ASW Batch was 0.186718906342356 prior to batch effect correction and is now -0.0377063484659106 .
2024-05-15 20:23:56.68954 INFO::ASW Label was 0.823308272749781 prior to batch effect correction and is now 0.945700718805968 .
2024-05-15 20:23:56.690289 INFO::Total function execution time is 0.0616731643676758 s and adjustment time is 0.0209274291992188 s ( 33.93 )
2024-05-15 20:23:56.691044 INFO::Formatting Data.
2024-05-15 20:23:56.691633 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:56.692559 INFO::Removing potential empty rows and columns
2024-05-15 20:23:56.693582 INFO::Found 0 missing values.
2024-05-15 20:23:56.694514 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.
2024-05-15 20:23:56.699447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:56.699999 INFO::Done
2024-05-15 20:23:56.700513 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:56.703693 INFO::Starting hierarchical adjustment
2024-05-15 20:23:56.704402 INFO::Found 2 batches.
2024-05-15 20:23:56.704929 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:56.70555 INFO::Using default BPPARAM
2024-05-15 20:23:56.706072 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:23:56.707036 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:23:56.725591 INFO::Done
2024-05-15 20:23:56.726267 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:56.729342 INFO::ASW Batch was 0.186718906342356 prior to batch effect correction and is now -0.0377063484659106 .
2024-05-15 20:23:56.729932 INFO::ASW Label was 0.823308272749781 prior to batch effect correction and is now 0.945700718805968 .
2024-05-15 20:23:56.730725 INFO::Total function execution time is 0.0396907329559326 s and adjustment time is 0.0213117599487305 s ( 53.69 )
2024-05-15 20:23:56.947224 INFO::Formatting Data.
2024-05-15 20:23:56.948252 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:56.949267 INFO::Removing potential empty rows and columns
2024-05-15 20:23:56.950455 INFO::Found 0 missing values.
2024-05-15 20:23:56.953507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:56.954038 INFO::Done
2024-05-15 20:23:56.954539 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:56.956894 INFO::Starting hierarchical adjustment
2024-05-15 20:23:56.957603 INFO::Found 3 batches.
2024-05-15 20:23:56.958102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:56.958781 INFO::Using default BPPARAM
2024-05-15 20:23:56.959288 INFO::Processing subtree level 1
2024-05-15 20:23:57.075265 INFO::Adjusting the last 1 batches sequentially
2024-05-15 20:23:57.077289 INFO::Done
2024-05-15 20:23:57.078021 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:57.080818 INFO::ASW Batch was -0.0487124042279995 prior to batch effect correction and is now -0.0487124042279995 .
2024-05-15 20:23:57.081931 INFO::Total function execution time is 0.135030746459961 s and adjustment time is 0.119793176651001 s ( 88.72 )
2024-05-15 20:23:57.08319 INFO::Formatting Data.
2024-05-15 20:23:57.083916 INFO::Typecasting input to dataframe.
2024-05-15 20:23:57.084737 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:57.085803 INFO::Removing potential empty rows and columns
2024-05-15 20:23:57.087042 INFO::Found 0 missing values.
2024-05-15 20:23:57.09039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:57.091002 INFO::Done
2024-05-15 20:23:57.091583 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:57.093834 INFO::Starting hierarchical adjustment
2024-05-15 20:23:57.09458 INFO::Found 3 batches.
2024-05-15 20:23:57.095171 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:57.095853 INFO::Using default BPPARAM
2024-05-15 20:23:57.096412 INFO::Processing subtree level 1
2024-05-15 20:23:57.190356 INFO::Adjusting the last 1 batches sequentially
2024-05-15 20:23:57.192567 INFO::Done
2024-05-15 20:23:57.193307 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:57.195958 INFO::ASW Batch was -0.0487124042279995 prior to batch effect correction and is now -0.0487124042279995 .
2024-05-15 20:23:57.196967 INFO::Total function execution time is 0.113774299621582 s and adjustment time is 0.0980749130249023 s ( 86.2 )
2024-05-15 20:23:57.210725 INFO::Formatting Data.
2024-05-15 20:23:57.211529 INFO::Typecasting input to dataframe.
2024-05-15 20:23:57.212447 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:57.213402 INFO::Removing potential empty rows and columns
2024-05-15 20:23:57.214546 INFO::Found 0 missing values.
2024-05-15 20:23:57.217663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:57.218296 INFO::Done
2024-05-15 20:23:57.218884 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:57.220944 INFO::Starting hierarchical adjustment
2024-05-15 20:23:57.221707 INFO::Found 3 batches.
2024-05-15 20:23:57.222278 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:57.223005 INFO::Using default BPPARAM
2024-05-15 20:23:57.223612 INFO::Processing subtree level 1
2024-05-15 20:23:57.317997 INFO::Adjusting the last 1 batches sequentially
2024-05-15 20:23:57.320072 INFO::Done
2024-05-15 20:23:57.321051 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:57.324075 INFO::ASW Batch was -0.0574468682478112 prior to batch effect correction and is now -0.0574468682478112 .
2024-05-15 20:23:57.325221 INFO::Total function execution time is 0.114518165588379 s and adjustment time is 0.0985085964202881 s ( 86.02 )
2024-05-15 20:23:57.489706 INFO::Formatting Data.
2024-05-15 20:23:57.490563 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:57.49181 INFO::Removing potential empty rows and columns
2024-05-15 20:23:57.49469 INFO::Found 1000 missing values.
2024-05-15 20:23:57.516971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:57.517967 INFO::Done
2024-05-15 20:23:57.518605 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:57.525013 INFO::Starting hierarchical adjustment
2024-05-15 20:23:57.525982 INFO::Found 10 batches.
2024-05-15 20:23:57.526535 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:23:57.527213 INFO::Using default BPPARAM
2024-05-15 20:23:57.527767 INFO::Processing subtree level 1
2024-05-15 20:23:57.671865 INFO::Processing subtree level 2
2024-05-15 20:23:57.885743 INFO::Adjusting the last 1 batches sequentially
2024-05-15 20:23:57.887573 INFO::Done
2024-05-15 20:23:57.888234 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:23:57.893944 INFO::ASW Batch was 0.461366815417236 prior to batch effect correction and is now 0.461366815417236 .
2024-05-15 20:23:57.894616 INFO::ASW Label was 0.343723729769381 prior to batch effect correction and is now 0.343723729769381 .
2024-05-15 20:23:57.895572 INFO::Total function execution time is 0.405938148498535 s and adjustment time is 0.361840009689331 s ( 89.14 )
2024-05-15 20:23:57.896458 INFO::Formatting Data.
2024-05-15 20:23:57.897102 INFO::Replacing NaNs with NAs.
2024-05-15 20:23:57.898303 INFO::Removing potential empty rows and columns
2024-05-15 20:23:57.901124 INFO::Found 1000 missing values.
2024-05-15 20:23:57.919517 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:23:57.920201 INFO::Done
2024-05-15 20:23:57.920733 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:23:57.926388 INFO::Starting hierarchical adjustment
2024-05-15 20:23:57.927178 INFO::Found 10 batches.
2024-05-15 20:23:59.026775 INFO::Set up parallel execution backend with 2 workers
2024-05-15 20:23:59.028445 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-15 20:24:00.134609 INFO::Adjusting the last 2 batches sequentially
2024-05-15 20:24:00.136467 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-15 20:24:00.15366 INFO::Done
2024-05-15 20:24:00.154292 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:24:00.159268 INFO::ASW Batch was 0.461366815417236 prior to batch effect correction and is now 0.461366815417236 .
2024-05-15 20:24:00.159873 INFO::ASW Label was 0.343723729769381 prior to batch effect correction and is now 0.343723729769381 .
2024-05-15 20:24:00.160639 INFO::Total function execution time is 2.26421427726746 s and adjustment time is 2.22661876678467 s ( 98.34 )
2024-05-15 20:24:00.292343 INFO::Formatting Data.
2024-05-15 20:24:00.293116 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.294052 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.295089 INFO::Found 0 missing values.
2024-05-15 20:24:00.298763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.299268 INFO::Done
2024-05-15 20:24:00.29974 INFO::Acquiring quality metrics before batch effect correction.
2024-05-15 20:24:00.302423 INFO::Starting hierarchical adjustment
2024-05-15 20:24:00.303066 INFO::Found 3 batches.
2024-05-15 20:24:00.303543 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-15 20:24:00.304114 INFO::Using default BPPARAM
2024-05-15 20:24:00.304593 INFO::Processing subtree level 1
2024-05-15 20:24:00.403809 INFO::Adjusting the last 1 batches sequentially
2024-05-15 20:24:00.405493 INFO::Done
2024-05-15 20:24:00.40611 INFO::Acquiring quality metrics after batch effect correction.
2024-05-15 20:24:00.409202 INFO::ASW Batch was 0.297905677583719 prior to batch effect correction and is now -0.136553884669885 .
2024-05-15 20:24:00.409798 INFO::ASW Label was -0.189190985218478 prior to batch effect correction and is now 0.136106761202621 .
2024-05-15 20:24:00.410672 INFO::Total function execution time is 0.118411064147949 s and adjustment time is 0.102529764175415 s ( 86.59 )
2024-05-15 20:24:00.521039 INFO::Formatting Data.
2024-05-15 20:24:00.521809 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.522652 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.523637 INFO::Found 2 missing values.
2024-05-15 20:24:00.526393 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.526893 INFO::Done
2024-05-15 20:24:00.552285 INFO::Found NA in Reference column
2024-05-15 20:24:00.561297 INFO::Require at least two references per batch.
2024-05-15 20:24:00.580077 INFO::Formatting Data.
2024-05-15 20:24:00.580772 INFO::Recognized SummarizedExperiment
2024-05-15 20:24:00.581314 INFO::Typecasting input to dataframe.
2024-05-15 20:24:00.590277 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.591336 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.594672 INFO::Found 0 missing values.
2024-05-15 20:24:00.601199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.601766 INFO::Done
2024-05-15 20:24:00.615882 INFO::Formatting Data.
2024-05-15 20:24:00.616503 INFO::Recognized SummarizedExperiment
2024-05-15 20:24:00.616962 INFO::Typecasting input to dataframe.
2024-05-15 20:24:00.632382 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.63348 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.636602 INFO::Found 0 missing values.
2024-05-15 20:24:00.646339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.646878 INFO::Done
2024-05-15 20:24:00.660265 INFO::Formatting Data.
2024-05-15 20:24:00.660891 INFO::Recognized SummarizedExperiment
2024-05-15 20:24:00.661376 INFO::Typecasting input to dataframe.
2024-05-15 20:24:00.676351 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.677316 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.678279 INFO::Found 0 missing values.
2024-05-15 20:24:00.679201 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.
2024-05-15 20:24:00.683199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.683732 INFO::Done
2024-05-15 20:24:00.692744 INFO::Formatting Data.
2024-05-15 20:24:00.693421 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.694192 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.695101 INFO::Found 0 missing values.
2024-05-15 20:24:00.697819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.698277 INFO::Done
2024-05-15 20:24:00.708047 INFO::Formatting Data.
2024-05-15 20:24:00.708694 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.709499 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.710381 INFO::Found 0 missing values.
2024-05-15 20:24:00.71289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.713397 INFO::Done
2024-05-15 20:24:00.738483 INFO::Formatting Data.
2024-05-15 20:24:00.739194 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.740113 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.741112 INFO::Found 1 missing values.
2024-05-15 20:24:00.743461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.743981 INFO::Done
2024-05-15 20:24:00.760162 INFO::Formatting Data.
2024-05-15 20:24:00.760849 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.76165 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.762516 INFO::Found 2 missing values.
2024-05-15 20:24:00.763333 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.
2024-05-15 20:24:00.765367 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.765836 INFO::Done
2024-05-15 20:24:00.774628 INFO::Formatting Data.
2024-05-15 20:24:00.775285 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.776082 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.77692 INFO::Found 2 missing values.
2024-05-15 20:24:00.778466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.778945 INFO::Done
2024-05-15 20:24:00.788244 INFO::Formatting Data.
2024-05-15 20:24:00.788917 INFO::Typecasting input to dataframe.
2024-05-15 20:24:00.789703 INFO::Replacing NaNs with NAs.
2024-05-15 20:24:00.79049 INFO::Removing potential empty rows and columns
2024-05-15 20:24:00.791401 INFO::Found 0 missing values.
2024-05-15 20:24:00.794079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-15 20:24:00.794566 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.632 3.540 19.839
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.623 | 1.299 | 17.765 | |
| compute_asw | 0.027 | 0.000 | 0.026 | |
| count_existing | 0.015 | 0.000 | 0.015 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.013 | 0.000 | 0.012 | |