Yannis Schumann
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 65b1ece |
| git_last_commit_date: 2024-02-28 02:41:28 -0400 (Wed, 28 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:21 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 155/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 0.99.16 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | 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: 0.99.16 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings BERT_0.99.16.tar.gz |
| StartedAt: 2024-03-28 03:07:12 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:08:33 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 81.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings BERT_0.99.16.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
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 ‘0.99.16’
* 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 30.49 1.565 22.162
* 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-4.4-devel-2024.03.20/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
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")
2024-03-28 03:08:18.833763 INFO::Formatting Data.
2024-03-28 03:08:18.835582 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:18.852605 INFO::Removing potential empty rows and columns
2024-03-28 03:08:19.223557 INFO::Found 0 missing values.
2024-03-28 03:08:19.228417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:19.229333 INFO::Done
2024-03-28 03:08:19.230148 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:19.245517 INFO::Starting hierarchical adjustment
2024-03-28 03:08:19.246679 INFO::Found 3 batches.
2024-03-28 03:08:19.247464 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:19.248979 INFO::Using default BPPARAM
2024-03-28 03:08:19.249797 INFO::Processing subtree level 1
2024-03-28 03:08:19.371541 INFO::Adjusting the last 1 batches sequentially
2024-03-28 03:08:19.373941 INFO::Done
2024-03-28 03:08:19.374905 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:19.378555 INFO::ASW Batch was -0.0873234901821814 prior to batch effect correction and is now -0.0873234901821814 .
2024-03-28 03:08:19.380162 INFO::Total function execution time is 0.547285079956055 s and adjustment time is 0.127496242523193 s ( 23.3 )
2024-03-28 03:08:19.401032 INFO::Formatting Data.
2024-03-28 03:08:19.402131 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:19.403602 INFO::Removing potential empty rows and columns
2024-03-28 03:08:19.40531 INFO::Found 0 missing values.
2024-03-28 03:08:19.406755 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.
2024-03-28 03:08:19.423801 INFO::Formatting Data.
2024-03-28 03:08:19.424994 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:19.426542 INFO::Removing potential empty rows and columns
2024-03-28 03:08:19.428345 INFO::Found 0 missing values.
2024-03-28 03:08:19.430097 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.
2024-03-28 03:08:19.454222 INFO::Formatting Data.
2024-03-28 03:08:19.455181 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:19.456385 INFO::Removing potential empty rows and columns
2024-03-28 03:08:19.457796 INFO::Found 0 missing values.
2024-03-28 03:08:19.459031 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.
2024-03-28 03:08:19.465193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:19.466027 INFO::Done
2024-03-28 03:08:19.466756 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:19.469534 INFO::Starting hierarchical adjustment
2024-03-28 03:08:19.47053 INFO::Found 2 batches.
2024-03-28 03:08:19.471304 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:19.472227 INFO::Using default BPPARAM
2024-03-28 03:08:19.47297 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:19.474278 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:19.502797 INFO::Done
2024-03-28 03:08:19.503658 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:19.506361 INFO::ASW Batch was -0.00140750474816139 prior to batch effect correction and is now -0.0952992489904693 .
2024-03-28 03:08:19.507482 INFO::Total function execution time is 0.053297758102417 s and adjustment time is 0.0324609279632568 s ( 60.9 )
2024-03-28 03:08:19.51124 INFO::Formatting Data.
2024-03-28 03:08:19.512147 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:19.524138 INFO::Formatting Data.
2024-03-28 03:08:19.525091 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:19.526277 INFO::Removing potential empty rows and columns
2024-03-28 03:08:19.52768 INFO::Found 0 missing values.
2024-03-28 03:08:19.531746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:19.532611 INFO::Done
2024-03-28 03:08:19.533328 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:19.536005 INFO::Starting hierarchical adjustment
2024-03-28 03:08:19.537031 INFO::Found 2 batches.
2024-03-28 03:08:19.537773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:19.538603 INFO::Using default BPPARAM
2024-03-28 03:08:19.539394 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:19.54069 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:19.560482 INFO::Done
2024-03-28 03:08:19.561311 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:19.563952 INFO::ASW Batch was -0.0197305130297229 prior to batch effect correction and is now -0.114943052807747 .
2024-03-28 03:08:19.565041 INFO::Total function execution time is 0.0409867763519287 s and adjustment time is 0.0236301422119141 s ( 57.65 )
2024-03-28 03:08:19.566462 INFO::Formatting Data.
2024-03-28 03:08:19.567292 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:19.568464 INFO::Removing potential empty rows and columns
2024-03-28 03:08:19.56986 INFO::Found 0 missing values.
2024-03-28 03:08:19.573879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:19.574658 INFO::Done
2024-03-28 03:08:19.575421 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:19.578046 INFO::Starting hierarchical adjustment
2024-03-28 03:08:19.579017 INFO::Found 2 batches.
2024-03-28 03:08:19.579781 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:19.580639 INFO::Using default BPPARAM
2024-03-28 03:08:19.581371 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:19.582616 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:19.602596 INFO::Done
2024-03-28 03:08:19.603447 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:19.606093 INFO::ASW Batch was -0.0197305130297229 prior to batch effect correction and is now -0.114943052807747 .
2024-03-28 03:08:19.607183 INFO::Total function execution time is 0.0406725406646729 s and adjustment time is 0.0237739086151123 s ( 58.45 )
2024-03-28 03:08:22.47087 INFO::Formatting Data.
2024-03-28 03:08:22.472002 INFO::Recognized SummarizedExperiment
2024-03-28 03:08:22.472681 INFO::Typecasting input to dataframe.
2024-03-28 03:08:22.557179 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:22.558632 INFO::Removing potential empty rows and columns
2024-03-28 03:08:22.563682 INFO::Found 0 missing values.
2024-03-28 03:08:22.573301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:22.574117 INFO::Done
2024-03-28 03:08:22.574806 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:22.579606 INFO::Starting hierarchical adjustment
2024-03-28 03:08:22.580654 INFO::Found 2 batches.
2024-03-28 03:08:22.581369 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:22.582726 INFO::Using default BPPARAM
2024-03-28 03:08:22.583463 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:22.584775 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:22.657541 INFO::Done
2024-03-28 03:08:22.658325 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:22.662878 INFO::ASW Batch was 0.00173905173847844 prior to batch effect correction and is now -0.0896245675604135 .
2024-03-28 03:08:22.664017 INFO::Total function execution time is 0.196849822998047 s and adjustment time is 0.0770895481109619 s ( 39.16 )
2024-03-28 03:08:22.686833 INFO::Formatting Data.
2024-03-28 03:08:22.687708 INFO::Recognized SummarizedExperiment
2024-03-28 03:08:22.688388 INFO::Typecasting input to dataframe.
2024-03-28 03:08:22.699784 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:22.701233 INFO::Removing potential empty rows and columns
2024-03-28 03:08:22.706019 INFO::Found 0 missing values.
2024-03-28 03:08:22.715419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:22.71622 INFO::Done
2024-03-28 03:08:22.716887 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:22.721352 INFO::Starting hierarchical adjustment
2024-03-28 03:08:22.72233 INFO::Found 2 batches.
2024-03-28 03:08:22.72302 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:22.723814 INFO::Using default BPPARAM
2024-03-28 03:08:22.724511 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:22.725807 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:22.758394 INFO::Done
2024-03-28 03:08:22.759219 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:22.763695 INFO::ASW Batch was -0.0100747392847379 prior to batch effect correction and is now -0.0100747392847379 .
2024-03-28 03:08:22.764817 INFO::Total function execution time is 0.0779414176940918 s and adjustment time is 0.0362339019775391 s ( 46.49 )
2024-03-28 03:08:22.78661 INFO::Formatting Data.
2024-03-28 03:08:22.787509 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:22.788599 INFO::Removing potential empty rows and columns
2024-03-28 03:08:22.789827 INFO::Found 0 missing values.
2024-03-28 03:08:22.793619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:22.79441 INFO::Done
2024-03-28 03:08:22.795115 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:22.797595 INFO::Starting hierarchical adjustment
2024-03-28 03:08:22.798579 INFO::Found 3 batches.
2024-03-28 03:08:22.799387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:22.80025 INFO::Using default BPPARAM
2024-03-28 03:08:22.800946 INFO::Processing subtree level 1
2024-03-28 03:08:22.985569 INFO::Adjusting the last 1 batches sequentially
2024-03-28 03:08:22.987937 INFO::Done
2024-03-28 03:08:22.988874 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:22.992299 INFO::ASW Batch was -0.111395223825564 prior to batch effect correction and is now -0.167528268547634 .
2024-03-28 03:08:22.993716 INFO::Total function execution time is 0.207022428512573 s and adjustment time is 0.189557552337646 s ( 91.56 )
2024-03-28 03:08:23.014464 INFO::Skipping initial DF formatting
2024-03-28 03:08:23.015425 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:23.021273 INFO::Starting hierarchical adjustment
2024-03-28 03:08:23.022385 INFO::Found 5 batches.
2024-03-28 03:08:23.023161 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:23.024067 INFO::Using default BPPARAM
2024-03-28 03:08:23.024832 INFO::Processing subtree level 1
2024-03-28 03:08:23.194877 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:23.197061 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:23.231185 INFO::Done
2024-03-28 03:08:23.232205 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:23.238379 INFO::ASW Batch was 0.5526236530007 prior to batch effect correction and is now 0.5526236530007 .
2024-03-28 03:08:23.239352 INFO::ASW Label was 0.321103367427251 prior to batch effect correction and is now 0.321103367427251 .
2024-03-28 03:08:23.240624 INFO::Total function execution time is 0.226169586181641 s and adjustment time is 0.208959579467773 s ( 92.39 )
2024-03-28 03:08:23.26719 INFO::Formatting Data.
2024-03-28 03:08:23.268263 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:23.269576 INFO::Removing potential empty rows and columns
2024-03-28 03:08:23.271055 INFO::Found 0 missing values.
2024-03-28 03:08:23.277519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:23.2784 INFO::Done
2024-03-28 03:08:23.27917 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:23.283431 INFO::Starting hierarchical adjustment
2024-03-28 03:08:23.284575 INFO::Found 5 batches.
2024-03-28 03:08:23.285367 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:23.286272 INFO::Using default BPPARAM
2024-03-28 03:08:23.287076 INFO::Processing subtree level 1
2024-03-28 03:08:23.426259 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:23.428293 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:23.45059 INFO::Done
2024-03-28 03:08:23.45154 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:23.455884 INFO::ASW Batch was 0.47508857932253 prior to batch effect correction and is now -0.109220213318937 .
2024-03-28 03:08:23.456805 INFO::ASW Label was 0.276502454953954 prior to batch effect correction and is now 0.892268225511622 .
2024-03-28 03:08:23.457941 INFO::Total function execution time is 0.190824747085571 s and adjustment time is 0.166250944137573 s ( 87.12 )
2024-03-28 03:08:23.459091 INFO::Formatting Data.
2024-03-28 03:08:23.459953 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:23.461208 INFO::Removing potential empty rows and columns
2024-03-28 03:08:23.462572 INFO::Found 0 missing values.
2024-03-28 03:08:23.468637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:23.46948 INFO::Done
2024-03-28 03:08:23.470228 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:23.474288 INFO::Starting hierarchical adjustment
2024-03-28 03:08:23.475354 INFO::Found 5 batches.
2024-03-28 03:08:23.476103 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:23.47701 INFO::Using default BPPARAM
2024-03-28 03:08:23.477777 INFO::Processing subtree level 1
2024-03-28 03:08:23.615338 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:23.617353 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:23.639055 INFO::Done
2024-03-28 03:08:23.639985 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:23.644294 INFO::ASW Batch was 0.47508857932253 prior to batch effect correction and is now -0.109220213318937 .
2024-03-28 03:08:23.645152 INFO::ASW Label was 0.276502454953954 prior to batch effect correction and is now 0.892268225511622 .
2024-03-28 03:08:23.646265 INFO::Total function execution time is 0.18718695640564 s and adjustment time is 0.163902282714844 s ( 87.56 )
2024-03-28 03:08:23.664942 INFO::Formatting Data.
2024-03-28 03:08:23.665935 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:23.667167 INFO::Removing potential empty rows and columns
2024-03-28 03:08:23.668549 INFO::Found 0 missing values.
2024-03-28 03:08:23.67452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:23.675391 INFO::Done
2024-03-28 03:08:23.676147 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:23.680344 INFO::Starting hierarchical adjustment
2024-03-28 03:08:23.681452 INFO::Found 5 batches.
2024-03-28 03:08:23.682235 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:23.683159 INFO::Using default BPPARAM
2024-03-28 03:08:23.683982 INFO::Processing subtree level 1
2024-03-28 03:08:23.820334 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:23.822486 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:23.84392 INFO::Done
2024-03-28 03:08:23.844826 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:23.849149 INFO::ASW Batch was 0.439737513132501 prior to batch effect correction and is now -0.0642797977525828 .
2024-03-28 03:08:23.850028 INFO::ASW Label was 0.382519298513655 prior to batch effect correction and is now 0.725343290369202 .
2024-03-28 03:08:23.851208 INFO::Total function execution time is 0.186274528503418 s and adjustment time is 0.162693500518799 s ( 87.34 )
2024-03-28 03:08:23.852396 INFO::Formatting Data.
2024-03-28 03:08:23.853289 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:23.854529 INFO::Removing potential empty rows and columns
2024-03-28 03:08:23.855984 INFO::Found 0 missing values.
2024-03-28 03:08:23.862121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:23.862979 INFO::Done
2024-03-28 03:08:23.863833 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:23.86798 INFO::Starting hierarchical adjustment
2024-03-28 03:08:23.869062 INFO::Found 5 batches.
2024-03-28 03:08:23.869851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:23.870739 INFO::Using default BPPARAM
2024-03-28 03:08:23.871553 INFO::Processing subtree level 1
2024-03-28 03:08:24.008783 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:24.010723 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:24.032521 INFO::Done
2024-03-28 03:08:24.033442 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:24.037794 INFO::ASW Batch was 0.439737513132501 prior to batch effect correction and is now -0.0642797977525828 .
2024-03-28 03:08:24.038655 INFO::ASW Label was 0.382519298513655 prior to batch effect correction and is now 0.725343290369202 .
2024-03-28 03:08:24.039843 INFO::Total function execution time is 0.187407732009888 s and adjustment time is 0.163657903671265 s ( 87.33 )
2024-03-28 03:08:24.058512 INFO::Formatting Data.
2024-03-28 03:08:24.059518 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:24.060796 INFO::Removing potential empty rows and columns
2024-03-28 03:08:24.062256 INFO::Found 0 missing values.
2024-03-28 03:08:24.066333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:24.070184 INFO::Done
2024-03-28 03:08:24.071125 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:24.075398 INFO::Starting hierarchical adjustment
2024-03-28 03:08:24.076543 INFO::Found 2 batches.
2024-03-28 03:08:24.077359 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:24.078281 INFO::Using default BPPARAM
2024-03-28 03:08:24.079089 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:24.080453 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:24.101347 INFO::Done
2024-03-28 03:08:24.102253 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:24.106431 INFO::ASW Batch was 0.613755360777925 prior to batch effect correction and is now 0.0512365304393451 .
2024-03-28 03:08:24.10734 INFO::ASW Label was 0.48468022151545 prior to batch effect correction and is now 0.866438189431779 .
2024-03-28 03:08:24.108528 INFO::Total function execution time is 0.0500397682189941 s and adjustment time is 0.0250318050384521 s ( 50.02 )
2024-03-28 03:08:24.109662 INFO::Formatting Data.
2024-03-28 03:08:24.110534 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:24.111792 INFO::Removing potential empty rows and columns
2024-03-28 03:08:24.113238 INFO::Found 0 missing values.
2024-03-28 03:08:24.117401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:24.118252 INFO::Done
2024-03-28 03:08:24.119092 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:24.123302 INFO::Starting hierarchical adjustment
2024-03-28 03:08:24.124402 INFO::Found 2 batches.
2024-03-28 03:08:24.12519 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:24.1261 INFO::Using default BPPARAM
2024-03-28 03:08:24.12687 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:24.128285 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:25.371274 INFO::Done
2024-03-28 03:08:25.372083 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:25.375748 INFO::ASW Batch was 0.613755360777925 prior to batch effect correction and is now 0.0512365304393451 .
2024-03-28 03:08:25.376547 INFO::ASW Label was 0.48468022151545 prior to batch effect correction and is now 0.866438189431779 .
2024-03-28 03:08:25.377494 INFO::Total function execution time is 1.26786494255066 s and adjustment time is 1.24712777137756 s ( 98.36 )
2024-03-28 03:08:25.390732 INFO::Formatting Data.
2024-03-28 03:08:25.391619 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:25.392664 INFO::Removing potential empty rows and columns
2024-03-28 03:08:25.393763 INFO::Found 0 missing values.
2024-03-28 03:08:25.396401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:25.39707 INFO::Done
2024-03-28 03:08:25.397712 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:25.400083 INFO::Starting hierarchical adjustment
2024-03-28 03:08:25.401042 INFO::Found 2 batches.
2024-03-28 03:08:25.40171 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:25.402466 INFO::Using default BPPARAM
2024-03-28 03:08:25.40315 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:25.404329 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:25.442283 INFO::Done
2024-03-28 03:08:25.443175 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:25.445753 INFO::ASW Batch was -0.0804954074243657 prior to batch effect correction and is now -0.148954838561908 .
2024-03-28 03:08:25.446862 INFO::Total function execution time is 0.0561556816101074 s and adjustment time is 0.0413975715637207 s ( 73.72 )
2024-03-28 03:08:25.461736 INFO::Formatting Data.
2024-03-28 03:08:25.462677 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:25.463848 INFO::Removing potential empty rows and columns
2024-03-28 03:08:25.465196 INFO::Found 0 missing values.
2024-03-28 03:08:25.46661 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.
2024-03-28 03:08:25.472825 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:25.473595 INFO::Done
2024-03-28 03:08:25.474284 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:25.478106 INFO::Starting hierarchical adjustment
2024-03-28 03:08:25.479092 INFO::Found 2 batches.
2024-03-28 03:08:25.479805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:25.480607 INFO::Using default BPPARAM
2024-03-28 03:08:25.481297 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:25.482543 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:25.502932 INFO::Done
2024-03-28 03:08:25.503772 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:25.507508 INFO::ASW Batch was 0.41127153917812 prior to batch effect correction and is now 0.0433651439051227 .
2024-03-28 03:08:25.50832 INFO::ASW Label was 0.642557730612736 prior to batch effect correction and is now 0.877422468046439 .
2024-03-28 03:08:25.509308 INFO::Total function execution time is 0.047621488571167 s and adjustment time is 0.0240421295166016 s ( 50.49 )
2024-03-28 03:08:25.510303 INFO::Formatting Data.
2024-03-28 03:08:25.511129 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:25.51234 INFO::Removing potential empty rows and columns
2024-03-28 03:08:25.513629 INFO::Found 0 missing values.
2024-03-28 03:08:25.514802 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.
2024-03-28 03:08:25.520975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:25.521741 INFO::Done
2024-03-28 03:08:25.522427 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:25.526264 INFO::Starting hierarchical adjustment
2024-03-28 03:08:25.527281 INFO::Found 2 batches.
2024-03-28 03:08:25.527997 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:25.528799 INFO::Using default BPPARAM
2024-03-28 03:08:25.529489 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:25.53071 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:25.551455 INFO::Done
2024-03-28 03:08:25.552355 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:25.556478 INFO::ASW Batch was 0.41127153917812 prior to batch effect correction and is now 0.0433651439051227 .
2024-03-28 03:08:25.55733 INFO::ASW Label was 0.642557730612736 prior to batch effect correction and is now 0.877422468046439 .
2024-03-28 03:08:25.558416 INFO::Total function execution time is 0.0481126308441162 s and adjustment time is 0.0243878364562988 s ( 50.69 )
2024-03-28 03:08:25.816265 INFO::Formatting Data.
2024-03-28 03:08:25.817126 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:25.818149 INFO::Removing potential empty rows and columns
2024-03-28 03:08:25.819376 INFO::Found 0 missing values.
2024-03-28 03:08:25.823093 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:25.82379 INFO::Done
2024-03-28 03:08:25.824445 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:25.826781 INFO::Starting hierarchical adjustment
2024-03-28 03:08:25.827666 INFO::Found 3 batches.
2024-03-28 03:08:25.828319 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:25.829046 INFO::Using default BPPARAM
2024-03-28 03:08:25.829692 INFO::Processing subtree level 1
2024-03-28 03:08:25.944896 INFO::Adjusting the last 1 batches sequentially
2024-03-28 03:08:25.947091 INFO::Done
2024-03-28 03:08:25.947871 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:25.950981 INFO::ASW Batch was -0.0561299907681827 prior to batch effect correction and is now -0.0561299907681827 .
2024-03-28 03:08:25.955415 INFO::Total function execution time is 0.139100313186646 s and adjustment time is 0.119573354721069 s ( 85.96 )
2024-03-28 03:08:25.957004 INFO::Formatting Data.
2024-03-28 03:08:25.958034 INFO::Typecasting input to dataframe.
2024-03-28 03:08:25.95912 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:25.960428 INFO::Removing potential empty rows and columns
2024-03-28 03:08:25.961926 INFO::Found 0 missing values.
2024-03-28 03:08:25.966569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:25.967405 INFO::Done
2024-03-28 03:08:25.96822 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:25.971169 INFO::Starting hierarchical adjustment
2024-03-28 03:08:25.972214 INFO::Found 3 batches.
2024-03-28 03:08:25.972976 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:25.973863 INFO::Using default BPPARAM
2024-03-28 03:08:25.974643 INFO::Processing subtree level 1
2024-03-28 03:08:26.093341 INFO::Adjusting the last 1 batches sequentially
2024-03-28 03:08:26.095602 INFO::Done
2024-03-28 03:08:26.096442 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:26.099776 INFO::ASW Batch was -0.0561299907681827 prior to batch effect correction and is now -0.0561299907681827 .
2024-03-28 03:08:26.101056 INFO::Total function execution time is 0.144065380096436 s and adjustment time is 0.123623609542847 s ( 85.81 )
2024-03-28 03:08:26.119003 INFO::Formatting Data.
2024-03-28 03:08:26.119985 INFO::Typecasting input to dataframe.
2024-03-28 03:08:26.121097 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:26.122275 INFO::Removing potential empty rows and columns
2024-03-28 03:08:26.12376 INFO::Found 0 missing values.
2024-03-28 03:08:26.128003 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:26.128814 INFO::Done
2024-03-28 03:08:26.12954 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:26.132249 INFO::Starting hierarchical adjustment
2024-03-28 03:08:26.133237 INFO::Found 3 batches.
2024-03-28 03:08:26.133959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:26.134811 INFO::Using default BPPARAM
2024-03-28 03:08:26.13559 INFO::Processing subtree level 1
2024-03-28 03:08:26.256286 INFO::Adjusting the last 1 batches sequentially
2024-03-28 03:08:26.258648 INFO::Done
2024-03-28 03:08:26.259539 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:26.262889 INFO::ASW Batch was -0.134043961324459 prior to batch effect correction and is now -0.134043961324459 .
2024-03-28 03:08:26.264308 INFO::Total function execution time is 0.145277738571167 s and adjustment time is 0.125597238540649 s ( 86.45 )
2024-03-28 03:08:26.451831 INFO::Formatting Data.
2024-03-28 03:08:26.452828 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:26.454278 INFO::Removing potential empty rows and columns
2024-03-28 03:08:26.458546 INFO::Found 1000 missing values.
2024-03-28 03:08:26.487647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:26.488535 INFO::Done
2024-03-28 03:08:26.489285 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:26.496918 INFO::Starting hierarchical adjustment
2024-03-28 03:08:26.498032 INFO::Found 10 batches.
2024-03-28 03:08:26.498768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:26.499632 INFO::Using default BPPARAM
2024-03-28 03:08:26.500388 INFO::Processing subtree level 1
2024-03-28 03:08:26.699753 INFO::Processing subtree level 2
2024-03-28 03:08:26.909167 INFO::Adjusting the last 1 batches sequentially
2024-03-28 03:08:26.911681 INFO::Done
2024-03-28 03:08:26.912635 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:26.920797 INFO::ASW Batch was 0.480422035194881 prior to batch effect correction and is now 0.480422035194881 .
2024-03-28 03:08:26.921822 INFO::ASW Label was 0.351793586347042 prior to batch effect correction and is now 0.351793586347042 .
2024-03-28 03:08:26.923165 INFO::Total function execution time is 0.471336603164673 s and adjustment time is 0.413874387741089 s ( 87.81 )
2024-03-28 03:08:26.924448 INFO::Formatting Data.
2024-03-28 03:08:26.925399 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:26.927201 INFO::Removing potential empty rows and columns
2024-03-28 03:08:26.932148 INFO::Found 1000 missing values.
2024-03-28 03:08:26.963185 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:26.96414 INFO::Done
2024-03-28 03:08:26.964934 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:26.972737 INFO::Starting hierarchical adjustment
2024-03-28 03:08:26.973889 INFO::Found 10 batches.
2024-03-28 03:08:28.10558 INFO::Set up parallel execution backend with 2 workers
2024-03-28 03:08:28.107317 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-03-28 03:08:29.424453 INFO::Adjusting the last 2 batches sequentially
2024-03-28 03:08:29.42628 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-28 03:08:29.451686 INFO::Done
2024-03-28 03:08:29.452536 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:29.459105 INFO::ASW Batch was 0.480422035194881 prior to batch effect correction and is now 0.480422035194881 .
2024-03-28 03:08:29.45992 INFO::ASW Label was 0.351793586347042 prior to batch effect correction and is now 0.351793586347042 .
2024-03-28 03:08:29.46095 INFO::Total function execution time is 2.53653812408447 s and adjustment time is 2.47802782058716 s ( 97.69 )
2024-03-28 03:08:29.648285 INFO::Formatting Data.
2024-03-28 03:08:29.649401 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:29.650945 INFO::Removing potential empty rows and columns
2024-03-28 03:08:29.652629 INFO::Found 0 missing values.
2024-03-28 03:08:29.658675 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:29.659565 INFO::Done
2024-03-28 03:08:29.660379 INFO::Acquiring quality metrics before batch effect correction.
2024-03-28 03:08:29.669977 INFO::Starting hierarchical adjustment
2024-03-28 03:08:29.671434 INFO::Found 3 batches.
2024-03-28 03:08:29.67238 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-28 03:08:29.673434 INFO::Using default BPPARAM
2024-03-28 03:08:29.674272 INFO::Processing subtree level 1
2024-03-28 03:08:29.805352 INFO::Adjusting the last 1 batches sequentially
2024-03-28 03:08:29.807935 INFO::Done
2024-03-28 03:08:29.80896 INFO::Acquiring quality metrics after batch effect correction.
2024-03-28 03:08:29.813948 INFO::ASW Batch was 0.296132553788983 prior to batch effect correction and is now -0.141516544920554 .
2024-03-28 03:08:29.814956 INFO::ASW Label was -0.222095296186618 prior to batch effect correction and is now -0.162424396319767 .
2024-03-28 03:08:29.816522 INFO::Total function execution time is 0.16825795173645 s and adjustment time is 0.136798858642578 s ( 81.3 )
2024-03-28 03:08:29.991717 INFO::Formatting Data.
2024-03-28 03:08:29.992721 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:29.993914 INFO::Removing potential empty rows and columns
2024-03-28 03:08:29.995396 INFO::Found 2 missing values.
2024-03-28 03:08:29.999681 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:30.000536 INFO::Done
2024-03-28 03:08:30.040184 INFO::Found NA in Reference column
2024-03-28 03:08:30.053855 INFO::Require at least two references per batch.
2024-03-28 03:08:30.083859 INFO::Formatting Data.
2024-03-28 03:08:30.0848 INFO::Recognized SummarizedExperiment
2024-03-28 03:08:30.085524 INFO::Typecasting input to dataframe.
2024-03-28 03:08:30.099727 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:30.101289 INFO::Removing potential empty rows and columns
2024-03-28 03:08:30.106826 INFO::Found 0 missing values.
2024-03-28 03:08:30.117689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:30.118511 INFO::Done
2024-03-28 03:08:30.140065 INFO::Formatting Data.
2024-03-28 03:08:30.140989 INFO::Recognized SummarizedExperiment
2024-03-28 03:08:30.141696 INFO::Typecasting input to dataframe.
2024-03-28 03:08:30.166912 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:30.168532 INFO::Removing potential empty rows and columns
2024-03-28 03:08:30.175207 INFO::Found 0 missing values.
2024-03-28 03:08:30.19426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:30.19521 INFO::Done
2024-03-28 03:08:30.219598 INFO::Formatting Data.
2024-03-28 03:08:30.220592 INFO::Recognized SummarizedExperiment
2024-03-28 03:08:30.221457 INFO::Typecasting input to dataframe.
2024-03-28 03:08:30.248923 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:30.250232 INFO::Removing potential empty rows and columns
2024-03-28 03:08:30.252613 INFO::Found 0 missing values.
2024-03-28 03:08:30.25411 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.
2024-03-28 03:08:30.261611 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:30.262423 INFO::Done
2024-03-28 03:08:30.276956 INFO::Formatting Data.
2024-03-28 03:08:30.277957 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:30.27918 INFO::Removing potential empty rows and columns
2024-03-28 03:08:30.280694 INFO::Found 0 missing values.
2024-03-28 03:08:30.285 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:30.285877 INFO::Done
2024-03-28 03:08:30.301546 INFO::Formatting Data.
2024-03-28 03:08:30.302666 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:30.303918 INFO::Removing potential empty rows and columns
2024-03-28 03:08:30.305371 INFO::Found 0 missing values.
2024-03-28 03:08:30.309788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:30.310706 INFO::Done
2024-03-28 03:08:30.35276 INFO::Formatting Data.
2024-03-28 03:08:30.353739 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:30.355147 INFO::Removing potential empty rows and columns
2024-03-28 03:08:30.356767 INFO::Found 1 missing values.
2024-03-28 03:08:30.360517 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:30.36135 INFO::Done
2024-03-28 03:08:30.388276 INFO::Formatting Data.
2024-03-28 03:08:30.389275 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:30.39045 INFO::Removing potential empty rows and columns
2024-03-28 03:08:30.391782 INFO::Found 2 missing values.
2024-03-28 03:08:30.39303 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.
2024-03-28 03:08:30.396315 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:30.397119 INFO::Done
2024-03-28 03:08:30.411381 INFO::Formatting Data.
2024-03-28 03:08:30.412372 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:30.41352 INFO::Removing potential empty rows and columns
2024-03-28 03:08:30.414861 INFO::Found 2 missing values.
2024-03-28 03:08:30.417136 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:30.417872 INFO::Done
2024-03-28 03:08:30.433403 INFO::Formatting Data.
2024-03-28 03:08:30.434469 INFO::Typecasting input to dataframe.
2024-03-28 03:08:30.435691 INFO::Replacing NaNs with NAs.
2024-03-28 03:08:30.436999 INFO::Removing potential empty rows and columns
2024-03-28 03:08:30.438496 INFO::Found 0 missing values.
2024-03-28 03:08:30.44416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-28 03:08:30.445089 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.922 4.226 25.778
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 30.490 | 1.565 | 22.162 | |
| compute_asw | 0.035 | 0.000 | 0.036 | |
| count_existing | 0.019 | 0.000 | 0.019 | |
| generate_data_covariables | 0.013 | 0.003 | 0.016 | |
| generate_dataset | 0.015 | 0.000 | 0.015 | |