Yannis Schumann
| Snapshot Date: 2024-10-17 13:40 -0400 (Thu, 17 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-18 11:48 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4474 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4733 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4509 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.1.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.1.2.tar.gz |
| StartedAt: 2024-10-18 02:54:50 -0000 (Fri, 18 Oct 2024) |
| EndedAt: 2024-10-18 02:56:10 -0000 (Fri, 18 Oct 2024) |
| EllapsedTime: 80.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.2’
* 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 31.363 1.882 23.116
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2024-10-18 02:55:55.294306 INFO::Formatting Data.
2024-10-18 02:55:55.296072 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:55.312927 INFO::Removing potential empty rows and columns
2024-10-18 02:55:55.685653 INFO::Found 0 missing values.
2024-10-18 02:55:55.690301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:55:55.691162 INFO::Done
2024-10-18 02:55:55.691882 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:55:55.706886 INFO::Starting hierarchical adjustment
2024-10-18 02:55:55.708044 INFO::Found 3 batches.
2024-10-18 02:55:55.708773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:55:55.710266 INFO::Using default BPPARAM
2024-10-18 02:55:55.711056 INFO::Processing subtree level 1
2024-10-18 02:55:55.842466 INFO::Adjusting the last 1 batches sequentially
2024-10-18 02:55:55.844848 INFO::Done
2024-10-18 02:55:55.845692 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:55:55.849237 INFO::ASW Batch was -0.0909897969230756 prior to batch effect correction and is now -0.0909897969230756 .
2024-10-18 02:55:55.850787 INFO::Total function execution time is 0.557254314422607 s and adjustment time is 0.137033224105835 s ( 24.59 )
2024-10-18 02:55:55.869509 INFO::Formatting Data.
2024-10-18 02:55:55.870445 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:55.871656 INFO::Removing potential empty rows and columns
2024-10-18 02:55:55.873067 INFO::Found 0 missing values.
2024-10-18 02:55:55.874275 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.
2024-10-18 02:55:55.888901 INFO::Formatting Data.
2024-10-18 02:55:55.88986 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:55.891027 INFO::Removing potential empty rows and columns
2024-10-18 02:55:55.892437 INFO::Found 0 missing values.
2024-10-18 02:55:55.893637 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.
2024-10-18 02:55:55.914801 INFO::Formatting Data.
2024-10-18 02:55:55.915779 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:55.916906 INFO::Removing potential empty rows and columns
2024-10-18 02:55:55.918269 INFO::Found 0 missing values.
2024-10-18 02:55:55.919511 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.
2024-10-18 02:55:55.925868 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:55:55.926715 INFO::Done
2024-10-18 02:55:55.927481 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:55:55.930182 INFO::Starting hierarchical adjustment
2024-10-18 02:55:55.931234 INFO::Found 2 batches.
2024-10-18 02:55:55.931963 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:55:55.932815 INFO::Using default BPPARAM
2024-10-18 02:55:55.93354 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:55:55.934826 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:55:55.970459 INFO::Done
2024-10-18 02:55:55.971442 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:55:55.974274 INFO::ASW Batch was 0.0550230853987097 prior to batch effect correction and is now -0.115171144285434 .
2024-10-18 02:55:55.975441 INFO::Total function execution time is 0.0606570243835449 s and adjustment time is 0.0394303798675537 s ( 65.01 )
2024-10-18 02:55:55.979249 INFO::Formatting Data.
2024-10-18 02:55:55.980191 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:55.993135 INFO::Formatting Data.
2024-10-18 02:55:55.994125 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:55.995385 INFO::Removing potential empty rows and columns
2024-10-18 02:55:55.99682 INFO::Found 0 missing values.
2024-10-18 02:55:56.001102 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:55:56.001982 INFO::Done
2024-10-18 02:55:56.00279 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:55:56.005643 INFO::Starting hierarchical adjustment
2024-10-18 02:55:56.006787 INFO::Found 2 batches.
2024-10-18 02:55:56.007653 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:55:56.008511 INFO::Using default BPPARAM
2024-10-18 02:55:56.009329 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:55:56.01071 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:55:56.031261 INFO::Done
2024-10-18 02:55:56.032123 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:55:56.034795 INFO::ASW Batch was -0.0377576907982727 prior to batch effect correction and is now -0.11474510644306 .
2024-10-18 02:55:56.035969 INFO::Total function execution time is 0.0428779125213623 s and adjustment time is 0.0246660709381104 s ( 57.53 )
2024-10-18 02:55:56.037421 INFO::Formatting Data.
2024-10-18 02:55:56.038251 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:56.039474 INFO::Removing potential empty rows and columns
2024-10-18 02:55:56.040903 INFO::Found 0 missing values.
2024-10-18 02:55:56.045012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:55:56.045878 INFO::Done
2024-10-18 02:55:56.046591 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:55:56.04938 INFO::Starting hierarchical adjustment
2024-10-18 02:55:56.050402 INFO::Found 2 batches.
2024-10-18 02:55:56.051187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:55:56.052024 INFO::Using default BPPARAM
2024-10-18 02:55:56.052739 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:55:56.054027 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:55:56.074208 INFO::Done
2024-10-18 02:55:56.075083 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:55:56.077864 INFO::ASW Batch was -0.0377576907982727 prior to batch effect correction and is now -0.11474510644306 .
2024-10-18 02:55:56.079014 INFO::Total function execution time is 0.0415709018707275 s and adjustment time is 0.0239932537078857 s ( 57.72 )
2024-10-18 02:55:59.04879 INFO::Formatting Data.
2024-10-18 02:55:59.049798 INFO::Recognized SummarizedExperiment
2024-10-18 02:55:59.050484 INFO::Typecasting input to dataframe.
2024-10-18 02:55:59.095816 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:59.097354 INFO::Removing potential empty rows and columns
2024-10-18 02:55:59.102765 INFO::Found 0 missing values.
2024-10-18 02:55:59.113232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:55:59.114082 INFO::Done
2024-10-18 02:55:59.114805 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:55:59.119939 INFO::Starting hierarchical adjustment
2024-10-18 02:55:59.121007 INFO::Found 2 batches.
2024-10-18 02:55:59.121712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:55:59.123168 INFO::Using default BPPARAM
2024-10-18 02:55:59.123946 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:55:59.125248 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:55:59.205236 INFO::Done
2024-10-18 02:55:59.206041 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:55:59.210722 INFO::ASW Batch was -0.0154634283564243 prior to batch effect correction and is now -0.0890097361591245 .
2024-10-18 02:55:59.211918 INFO::Total function execution time is 0.163756370544434 s and adjustment time is 0.0844383239746094 s ( 51.56 )
2024-10-18 02:55:59.235732 INFO::Formatting Data.
2024-10-18 02:55:59.236607 INFO::Recognized SummarizedExperiment
2024-10-18 02:55:59.237296 INFO::Typecasting input to dataframe.
2024-10-18 02:55:59.249926 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:59.251539 INFO::Removing potential empty rows and columns
2024-10-18 02:55:59.256926 INFO::Found 0 missing values.
2024-10-18 02:55:59.267471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:55:59.268341 INFO::Done
2024-10-18 02:55:59.269082 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:55:59.274004 INFO::Starting hierarchical adjustment
2024-10-18 02:55:59.275139 INFO::Found 2 batches.
2024-10-18 02:55:59.275933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:55:59.276751 INFO::Using default BPPARAM
2024-10-18 02:55:59.277467 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:55:59.27882 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:55:59.313438 INFO::Done
2024-10-18 02:55:59.314275 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:55:59.318974 INFO::ASW Batch was 0.0156876655930336 prior to batch effect correction and is now 0.0156876655930336 .
2024-10-18 02:55:59.320174 INFO::Total function execution time is 0.0843977928161621 s and adjustment time is 0.0385417938232422 s ( 45.67 )
2024-10-18 02:55:59.343433 INFO::Formatting Data.
2024-10-18 02:55:59.344365 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:59.345437 INFO::Removing potential empty rows and columns
2024-10-18 02:55:59.346734 INFO::Found 0 missing values.
2024-10-18 02:55:59.350657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:55:59.351497 INFO::Done
2024-10-18 02:55:59.352182 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:55:59.354642 INFO::Starting hierarchical adjustment
2024-10-18 02:55:59.355582 INFO::Found 3 batches.
2024-10-18 02:55:59.356247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:55:59.356997 INFO::Using default BPPARAM
2024-10-18 02:55:59.35764 INFO::Processing subtree level 1
2024-10-18 02:55:59.571639 INFO::Adjusting the last 1 batches sequentially
2024-10-18 02:55:59.574153 INFO::Done
2024-10-18 02:55:59.57514 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:55:59.578811 INFO::ASW Batch was -0.00906112858699639 prior to batch effect correction and is now -0.178195371021921 .
2024-10-18 02:55:59.580311 INFO::Total function execution time is 0.23686957359314 s and adjustment time is 0.218724250793457 s ( 92.34 )
2024-10-18 02:55:59.603654 INFO::Skipping initial DF formatting
2024-10-18 02:55:59.604777 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:55:59.611008 INFO::Starting hierarchical adjustment
2024-10-18 02:55:59.612229 INFO::Found 5 batches.
2024-10-18 02:55:59.613022 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:55:59.613955 INFO::Using default BPPARAM
2024-10-18 02:55:59.61471 INFO::Processing subtree level 1
2024-10-18 02:55:59.791347 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:55:59.793636 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:55:59.825678 INFO::Done
2024-10-18 02:55:59.826629 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:55:59.833085 INFO::ASW Batch was 0.557306676537659 prior to batch effect correction and is now 0.557306676537659 .
2024-10-18 02:55:59.834059 INFO::ASW Label was 0.353563014562816 prior to batch effect correction and is now 0.353563014562816 .
2024-10-18 02:55:59.835405 INFO::Total function execution time is 0.231788873672485 s and adjustment time is 0.213660001754761 s ( 92.18 )
2024-10-18 02:55:59.862733 INFO::Formatting Data.
2024-10-18 02:55:59.863865 INFO::Replacing NaNs with NAs.
2024-10-18 02:55:59.86522 INFO::Removing potential empty rows and columns
2024-10-18 02:55:59.866719 INFO::Found 0 missing values.
2024-10-18 02:55:59.873049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:55:59.873976 INFO::Done
2024-10-18 02:55:59.874757 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:55:59.879135 INFO::Starting hierarchical adjustment
2024-10-18 02:55:59.880328 INFO::Found 5 batches.
2024-10-18 02:55:59.881112 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:55:59.881993 INFO::Using default BPPARAM
2024-10-18 02:55:59.882739 INFO::Processing subtree level 1
2024-10-18 02:56:00.033916 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:56:00.03598 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:56:00.059327 INFO::Done
2024-10-18 02:56:00.060267 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:00.064728 INFO::ASW Batch was 0.398833025558919 prior to batch effect correction and is now -0.0889712210083733 .
2024-10-18 02:56:00.065625 INFO::ASW Label was 0.268815177193688 prior to batch effect correction and is now 0.861378404046037 .
2024-10-18 02:56:00.06677 INFO::Total function execution time is 0.204117298126221 s and adjustment time is 0.179201126098633 s ( 87.79 )
2024-10-18 02:56:00.067993 INFO::Formatting Data.
2024-10-18 02:56:00.068891 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:00.07016 INFO::Removing potential empty rows and columns
2024-10-18 02:56:00.071628 INFO::Found 0 missing values.
2024-10-18 02:56:00.077684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:00.078579 INFO::Done
2024-10-18 02:56:00.079352 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:00.083459 INFO::Starting hierarchical adjustment
2024-10-18 02:56:00.084727 INFO::Found 5 batches.
2024-10-18 02:56:00.085498 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:00.086392 INFO::Using default BPPARAM
2024-10-18 02:56:00.087151 INFO::Processing subtree level 1
2024-10-18 02:56:00.246638 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:56:00.248868 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:56:00.270583 INFO::Done
2024-10-18 02:56:00.27154 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:00.275981 INFO::ASW Batch was 0.398833025558919 prior to batch effect correction and is now -0.0889712210083733 .
2024-10-18 02:56:00.276872 INFO::ASW Label was 0.268815177193688 prior to batch effect correction and is now 0.861378404046037 .
2024-10-18 02:56:00.278025 INFO::Total function execution time is 0.210024118423462 s and adjustment time is 0.186105966567993 s ( 88.61 )
2024-10-18 02:56:00.297185 INFO::Formatting Data.
2024-10-18 02:56:00.298201 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:00.29949 INFO::Removing potential empty rows and columns
2024-10-18 02:56:00.300861 INFO::Found 0 missing values.
2024-10-18 02:56:00.306879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:00.307822 INFO::Done
2024-10-18 02:56:00.308553 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:00.31268 INFO::Starting hierarchical adjustment
2024-10-18 02:56:00.313742 INFO::Found 5 batches.
2024-10-18 02:56:00.31451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:00.31547 INFO::Using default BPPARAM
2024-10-18 02:56:00.316232 INFO::Processing subtree level 1
2024-10-18 02:56:00.515768 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:56:00.517892 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:56:00.540562 INFO::Done
2024-10-18 02:56:00.541484 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:00.546028 INFO::ASW Batch was 0.218032881474491 prior to batch effect correction and is now -0.0374352611429027 .
2024-10-18 02:56:00.546966 INFO::ASW Label was 0.519133298190065 prior to batch effect correction and is now 0.822631689569257 .
2024-10-18 02:56:00.548168 INFO::Total function execution time is 0.251027822494507 s and adjustment time is 0.227025032043457 s ( 90.44 )
2024-10-18 02:56:00.549353 INFO::Formatting Data.
2024-10-18 02:56:00.550186 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:00.551475 INFO::Removing potential empty rows and columns
2024-10-18 02:56:00.552922 INFO::Found 0 missing values.
2024-10-18 02:56:00.559096 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:00.559987 INFO::Done
2024-10-18 02:56:00.560724 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:00.597979 INFO::Starting hierarchical adjustment
2024-10-18 02:56:00.599199 INFO::Found 5 batches.
2024-10-18 02:56:00.599989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:00.600879 INFO::Using default BPPARAM
2024-10-18 02:56:00.601641 INFO::Processing subtree level 1
2024-10-18 02:56:00.765178 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:56:00.767458 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:56:00.792712 INFO::Done
2024-10-18 02:56:00.793748 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:00.798793 INFO::ASW Batch was 0.218032881474491 prior to batch effect correction and is now -0.0374352611429027 .
2024-10-18 02:56:00.799803 INFO::ASW Label was 0.519133298190065 prior to batch effect correction and is now 0.822631689569257 .
2024-10-18 02:56:00.800993 INFO::Total function execution time is 0.251612663269043 s and adjustment time is 0.193784236907959 s ( 77.02 )
2024-10-18 02:56:00.826079 INFO::Formatting Data.
2024-10-18 02:56:00.827365 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:00.828799 INFO::Removing potential empty rows and columns
2024-10-18 02:56:00.830452 INFO::Found 0 missing values.
2024-10-18 02:56:00.835345 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:00.836263 INFO::Done
2024-10-18 02:56:00.837012 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:00.841783 INFO::Starting hierarchical adjustment
2024-10-18 02:56:00.843024 INFO::Found 2 batches.
2024-10-18 02:56:00.843841 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:00.844741 INFO::Using default BPPARAM
2024-10-18 02:56:00.845514 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:56:00.846901 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:56:00.870705 INFO::Done
2024-10-18 02:56:00.871724 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:00.876722 INFO::ASW Batch was 0.52036842672022 prior to batch effect correction and is now 0.118152687778193 .
2024-10-18 02:56:00.877759 INFO::ASW Label was 0.595771568575064 prior to batch effect correction and is now 0.831854450769186 .
2024-10-18 02:56:00.879034 INFO::Total function execution time is 0.0530726909637451 s and adjustment time is 0.0279583930969238 s ( 52.68 )
2024-10-18 02:56:00.880323 INFO::Formatting Data.
2024-10-18 02:56:00.881325 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:00.882657 INFO::Removing potential empty rows and columns
2024-10-18 02:56:00.884389 INFO::Found 0 missing values.
2024-10-18 02:56:00.888986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:00.889931 INFO::Done
2024-10-18 02:56:00.890788 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:00.895615 INFO::Starting hierarchical adjustment
2024-10-18 02:56:00.896768 INFO::Found 2 batches.
2024-10-18 02:56:00.897573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:00.898441 INFO::Using default BPPARAM
2024-10-18 02:56:00.899241 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:56:00.900628 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:56:00.923487 INFO::Done
2024-10-18 02:56:00.92439 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:00.928746 INFO::ASW Batch was 0.52036842672022 prior to batch effect correction and is now 0.118152687778193 .
2024-10-18 02:56:00.929688 INFO::ASW Label was 0.595771568575064 prior to batch effect correction and is now 0.831854450769186 .
2024-10-18 02:56:00.930812 INFO::Total function execution time is 0.0505249500274658 s and adjustment time is 0.02693772315979 s ( 53.32 )
2024-10-18 02:56:00.948034 INFO::Formatting Data.
2024-10-18 02:56:00.949024 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:00.950216 INFO::Removing potential empty rows and columns
2024-10-18 02:56:00.951557 INFO::Found 0 missing values.
2024-10-18 02:56:00.954744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:00.955596 INFO::Done
2024-10-18 02:56:00.956336 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:00.959117 INFO::Starting hierarchical adjustment
2024-10-18 02:56:00.960203 INFO::Found 2 batches.
2024-10-18 02:56:00.960939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:00.961857 INFO::Using default BPPARAM
2024-10-18 02:56:00.962667 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:56:00.964202 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:56:01.013159 INFO::Done
2024-10-18 02:56:01.014161 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:01.01723 INFO::ASW Batch was -0.0173519965684143 prior to batch effect correction and is now -0.0664146768915031 .
2024-10-18 02:56:01.018666 INFO::Total function execution time is 0.0706632137298584 s and adjustment time is 0.0531477928161621 s ( 75.21 )
2024-10-18 02:56:01.03813 INFO::Formatting Data.
2024-10-18 02:56:01.039264 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:01.040663 INFO::Removing potential empty rows and columns
2024-10-18 02:56:01.042204 INFO::Found 0 missing values.
2024-10-18 02:56:01.044081 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.
2024-10-18 02:56:01.051515 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:01.052431 INFO::Done
2024-10-18 02:56:01.053267 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:01.057571 INFO::Starting hierarchical adjustment
2024-10-18 02:56:01.058703 INFO::Found 2 batches.
2024-10-18 02:56:01.059606 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:01.060561 INFO::Using default BPPARAM
2024-10-18 02:56:01.061291 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:56:01.062656 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:56:01.088037 INFO::Done
2024-10-18 02:56:01.088944 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:01.093207 INFO::ASW Batch was 0.305587929085202 prior to batch effect correction and is now -0.0375475529567399 .
2024-10-18 02:56:01.094154 INFO::ASW Label was 0.725117532735869 prior to batch effect correction and is now 0.952660454646577 .
2024-10-18 02:56:01.095284 INFO::Total function execution time is 0.0572717189788818 s and adjustment time is 0.0295374393463135 s ( 51.57 )
2024-10-18 02:56:01.096475 INFO::Formatting Data.
2024-10-18 02:56:01.097364 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:01.09886 INFO::Removing potential empty rows and columns
2024-10-18 02:56:01.100678 INFO::Found 0 missing values.
2024-10-18 02:56:01.10206 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.
2024-10-18 02:56:01.109188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:01.110083 INFO::Done
2024-10-18 02:56:01.110836 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:01.114987 INFO::Starting hierarchical adjustment
2024-10-18 02:56:01.116128 INFO::Found 2 batches.
2024-10-18 02:56:01.116883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:01.117728 INFO::Using default BPPARAM
2024-10-18 02:56:01.118482 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:56:01.119911 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:56:01.143924 INFO::Done
2024-10-18 02:56:01.144852 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:01.149079 INFO::ASW Batch was 0.305587929085202 prior to batch effect correction and is now -0.0375475529567399 .
2024-10-18 02:56:01.149961 INFO::ASW Label was 0.725117532735869 prior to batch effect correction and is now 0.952660454646577 .
2024-10-18 02:56:01.15109 INFO::Total function execution time is 0.0546374320983887 s and adjustment time is 0.0280041694641113 s ( 51.25 )
2024-10-18 02:56:01.479661 INFO::Formatting Data.
2024-10-18 02:56:01.48065 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:01.48187 INFO::Removing potential empty rows and columns
2024-10-18 02:56:01.483382 INFO::Found 0 missing values.
2024-10-18 02:56:01.488013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:01.488923 INFO::Done
2024-10-18 02:56:01.489676 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:01.492525 INFO::Starting hierarchical adjustment
2024-10-18 02:56:01.493602 INFO::Found 3 batches.
2024-10-18 02:56:01.494353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:01.495409 INFO::Using default BPPARAM
2024-10-18 02:56:01.496316 INFO::Processing subtree level 1
2024-10-18 02:56:01.708284 INFO::Adjusting the last 1 batches sequentially
2024-10-18 02:56:01.710664 INFO::Done
2024-10-18 02:56:01.711589 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:01.715089 INFO::ASW Batch was -0.0369244476044464 prior to batch effect correction and is now -0.0369244476044464 .
2024-10-18 02:56:01.716548 INFO::Total function execution time is 0.236882209777832 s and adjustment time is 0.217265129089355 s ( 91.72 )
2024-10-18 02:56:01.718107 INFO::Formatting Data.
2024-10-18 02:56:01.719077 INFO::Typecasting input to dataframe.
2024-10-18 02:56:01.720213 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:01.721569 INFO::Removing potential empty rows and columns
2024-10-18 02:56:01.723251 INFO::Found 0 missing values.
2024-10-18 02:56:01.728043 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:01.728956 INFO::Done
2024-10-18 02:56:01.729753 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:01.732649 INFO::Starting hierarchical adjustment
2024-10-18 02:56:01.733778 INFO::Found 3 batches.
2024-10-18 02:56:01.734575 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:01.735579 INFO::Using default BPPARAM
2024-10-18 02:56:01.736381 INFO::Processing subtree level 1
2024-10-18 02:56:01.954736 INFO::Adjusting the last 1 batches sequentially
2024-10-18 02:56:01.957107 INFO::Done
2024-10-18 02:56:01.957974 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:01.961488 INFO::ASW Batch was -0.0369244476044464 prior to batch effect correction and is now -0.0369244476044464 .
2024-10-18 02:56:01.962989 INFO::Total function execution time is 0.244834661483765 s and adjustment time is 0.223546743392944 s ( 91.31 )
2024-10-18 02:56:01.982449 INFO::Formatting Data.
2024-10-18 02:56:01.983583 INFO::Typecasting input to dataframe.
2024-10-18 02:56:01.984839 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:01.986156 INFO::Removing potential empty rows and columns
2024-10-18 02:56:01.987805 INFO::Found 0 missing values.
2024-10-18 02:56:01.992509 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:01.993419 INFO::Done
2024-10-18 02:56:01.9942 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:01.997119 INFO::Starting hierarchical adjustment
2024-10-18 02:56:01.998239 INFO::Found 3 batches.
2024-10-18 02:56:01.999055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:02.000003 INFO::Using default BPPARAM
2024-10-18 02:56:02.00078 INFO::Processing subtree level 1
2024-10-18 02:56:02.179993 INFO::Adjusting the last 1 batches sequentially
2024-10-18 02:56:02.185513 INFO::Done
2024-10-18 02:56:02.186503 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:02.190711 INFO::ASW Batch was -0.0404726377900737 prior to batch effect correction and is now -0.0404726377900737 .
2024-10-18 02:56:02.192227 INFO::Total function execution time is 0.209794044494629 s and adjustment time is 0.187468290328979 s ( 89.36 )
2024-10-18 02:56:02.420096 INFO::Formatting Data.
2024-10-18 02:56:02.421265 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:02.42315 INFO::Removing potential empty rows and columns
2024-10-18 02:56:02.428267 INFO::Found 1000 missing values.
2024-10-18 02:56:02.463681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:02.464911 INFO::Done
2024-10-18 02:56:02.465696 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:02.474159 INFO::Starting hierarchical adjustment
2024-10-18 02:56:02.475381 INFO::Found 10 batches.
2024-10-18 02:56:02.476194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:02.477204 INFO::Using default BPPARAM
2024-10-18 02:56:02.477964 INFO::Processing subtree level 1
2024-10-18 02:56:02.686978 INFO::Processing subtree level 2
2024-10-18 02:56:02.927472 INFO::Adjusting the last 1 batches sequentially
2024-10-18 02:56:02.930322 INFO::Done
2024-10-18 02:56:02.931452 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:02.940506 INFO::ASW Batch was 0.52117348235054 prior to batch effect correction and is now 0.52117348235054 .
2024-10-18 02:56:02.941554 INFO::ASW Label was 0.30492226458282 prior to batch effect correction and is now 0.30492226458282 .
2024-10-18 02:56:02.943069 INFO::Total function execution time is 0.522934913635254 s and adjustment time is 0.455181837081909 s ( 87.04 )
2024-10-18 02:56:02.944481 INFO::Formatting Data.
2024-10-18 02:56:02.945534 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:02.947787 INFO::Removing potential empty rows and columns
2024-10-18 02:56:02.952886 INFO::Found 1000 missing values.
2024-10-18 02:56:02.986705 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:02.987768 INFO::Done
2024-10-18 02:56:02.988638 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:02.996956 INFO::Starting hierarchical adjustment
2024-10-18 02:56:02.998207 INFO::Found 10 batches.
2024-10-18 02:56:04.437429 INFO::Set up parallel execution backend with 2 workers
2024-10-18 02:56:04.438609 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-18 02:56:05.951098 INFO::Adjusting the last 2 batches sequentially
2024-10-18 02:56:05.953097 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-18 02:56:05.979511 INFO::Done
2024-10-18 02:56:05.980341 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:05.987163 INFO::ASW Batch was 0.52117348235054 prior to batch effect correction and is now 0.52117348235054 .
2024-10-18 02:56:05.988027 INFO::ASW Label was 0.30492226458282 prior to batch effect correction and is now 0.30492226458282 .
2024-10-18 02:56:05.989034 INFO::Total function execution time is 3.04465055465698 s and adjustment time is 2.98156261444092 s ( 97.93 )
2024-10-18 02:56:06.178127 INFO::Formatting Data.
2024-10-18 02:56:06.179235 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.180594 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.182168 INFO::Found 0 missing values.
2024-10-18 02:56:06.187966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.188854 INFO::Done
2024-10-18 02:56:06.18959 INFO::Acquiring quality metrics before batch effect correction.
2024-10-18 02:56:06.193581 INFO::Starting hierarchical adjustment
2024-10-18 02:56:06.194726 INFO::Found 3 batches.
2024-10-18 02:56:06.195558 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-18 02:56:06.196433 INFO::Using default BPPARAM
2024-10-18 02:56:06.197159 INFO::Processing subtree level 1
2024-10-18 02:56:06.33386 INFO::Adjusting the last 1 batches sequentially
2024-10-18 02:56:06.336351 INFO::Done
2024-10-18 02:56:06.337325 INFO::Acquiring quality metrics after batch effect correction.
2024-10-18 02:56:06.342283 INFO::ASW Batch was 0.182180869760913 prior to batch effect correction and is now -0.125678033610236 .
2024-10-18 02:56:06.343355 INFO::ASW Label was -0.196855124164292 prior to batch effect correction and is now -0.0210613595120847 .
2024-10-18 02:56:06.34473 INFO::Total function execution time is 0.166595458984375 s and adjustment time is 0.141823053359985 s ( 85.13 )
2024-10-18 02:56:06.517216 INFO::Formatting Data.
2024-10-18 02:56:06.518257 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.519564 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.521142 INFO::Found 2 missing values.
2024-10-18 02:56:06.52557 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.526454 INFO::Done
2024-10-18 02:56:06.567035 INFO::Found NA in Reference column
2024-10-18 02:56:06.581369 INFO::Require at least two references per batch.
2024-10-18 02:56:06.611778 INFO::Formatting Data.
2024-10-18 02:56:06.612736 INFO::Recognized SummarizedExperiment
2024-10-18 02:56:06.613473 INFO::Typecasting input to dataframe.
2024-10-18 02:56:06.628267 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.62988 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.635881 INFO::Found 0 missing values.
2024-10-18 02:56:06.647546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.648454 INFO::Done
2024-10-18 02:56:06.671863 INFO::Formatting Data.
2024-10-18 02:56:06.672835 INFO::Recognized SummarizedExperiment
2024-10-18 02:56:06.673591 INFO::Typecasting input to dataframe.
2024-10-18 02:56:06.700139 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.70177 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.707508 INFO::Found 0 missing values.
2024-10-18 02:56:06.725927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.726847 INFO::Done
2024-10-18 02:56:06.749074 INFO::Formatting Data.
2024-10-18 02:56:06.750002 INFO::Recognized SummarizedExperiment
2024-10-18 02:56:06.750728 INFO::Typecasting input to dataframe.
2024-10-18 02:56:06.776448 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.777794 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.779418 INFO::Found 0 missing values.
2024-10-18 02:56:06.780722 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.
2024-10-18 02:56:06.787503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.788375 INFO::Done
2024-10-18 02:56:06.802446 INFO::Formatting Data.
2024-10-18 02:56:06.803512 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.804697 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.806112 INFO::Found 0 missing values.
2024-10-18 02:56:06.81134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.812228 INFO::Done
2024-10-18 02:56:06.828395 INFO::Formatting Data.
2024-10-18 02:56:06.829463 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.830695 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.832268 INFO::Found 0 missing values.
2024-10-18 02:56:06.836603 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.837478 INFO::Done
2024-10-18 02:56:06.88044 INFO::Formatting Data.
2024-10-18 02:56:06.881521 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.883019 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.885027 INFO::Found 1 missing values.
2024-10-18 02:56:06.889771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.890682 INFO::Done
2024-10-18 02:56:06.91797 INFO::Formatting Data.
2024-10-18 02:56:06.919044 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.920326 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.921753 INFO::Found 2 missing values.
2024-10-18 02:56:06.923069 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.
2024-10-18 02:56:06.92656 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.927503 INFO::Done
2024-10-18 02:56:06.94231 INFO::Formatting Data.
2024-10-18 02:56:06.943403 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.944679 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.946048 INFO::Found 2 missing values.
2024-10-18 02:56:06.9487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.949674 INFO::Done
2024-10-18 02:56:06.966289 INFO::Formatting Data.
2024-10-18 02:56:06.967436 INFO::Typecasting input to dataframe.
2024-10-18 02:56:06.968698 INFO::Replacing NaNs with NAs.
2024-10-18 02:56:06.969912 INFO::Removing potential empty rows and columns
2024-10-18 02:56:06.971489 INFO::Found 0 missing values.
2024-10-18 02:56:06.976326 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-18 02:56:06.977272 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.757 5.044 26.182
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.363 | 1.882 | 23.116 | |
| compute_asw | 0.036 | 0.001 | 0.036 | |
| count_existing | 0.02 | 0.00 | 0.02 | |
| generate_data_covariables | 0.017 | 0.000 | 0.018 | |
| generate_dataset | 0.017 | 0.000 | 0.017 | |