Yannis Schumann
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:40 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (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 | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.0.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-06-10 00:47:23 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 00:54:15 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 412.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.0.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BERT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 7.83 4.69 28.45
* 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: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'BERT' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2024-06-10 00:50:14.667174 INFO::Formatting Data.
2024-06-10 00:50:14.682303 INFO::Replacing NaNs with NAs.
2024-06-10 00:50:14.698741 INFO::Removing potential empty rows and columns
2024-06-10 00:50:15.316801 INFO::Found 0 missing values.
2024-06-10 00:50:15.320058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:50:15.321414 INFO::Done
2024-06-10 00:50:15.322722 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:50:15.390933 INFO::Starting hierarchical adjustment
2024-06-10 00:50:15.392782 INFO::Found 3 batches.
2024-06-10 00:50:15.394251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:50:15.396444 INFO::Using default BPPARAM
2024-06-10 00:50:15.397823 INFO::Processing subtree level 1
2024-06-10 00:50:27.911178 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:50:27.913414 INFO::Done
2024-06-10 00:50:27.914806 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:50:27.918073 INFO::ASW Batch was -0.0737833511008707 prior to batch effect correction and is now -0.0737833511008707 .
2024-06-10 00:50:27.919734 INFO::Total function execution time is 13.2533299922943 s and adjustment time is 12.5209329128265 s ( 94.47 )
2024-06-10 00:50:27.942148 INFO::Formatting Data.
2024-06-10 00:50:27.943557 INFO::Replacing NaNs with NAs.
2024-06-10 00:50:27.945242 INFO::Removing potential empty rows and columns
2024-06-10 00:50:27.946914 INFO::Found 0 missing values.
2024-06-10 00:50:27.94843 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.
2024-06-10 00:50:27.961267 INFO::Formatting Data.
2024-06-10 00:50:27.962594 INFO::Replacing NaNs with NAs.
2024-06-10 00:50:27.964132 INFO::Removing potential empty rows and columns
2024-06-10 00:50:27.965739 INFO::Found 0 missing values.
2024-06-10 00:50:27.967264 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.
2024-06-10 00:50:27.99118 INFO::Formatting Data.
2024-06-10 00:50:27.992661 INFO::Replacing NaNs with NAs.
2024-06-10 00:50:27.994542 INFO::Removing potential empty rows and columns
2024-06-10 00:50:27.996462 INFO::Found 0 missing values.
2024-06-10 00:50:27.997949 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.
2024-06-10 00:50:28.00441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:50:28.005581 INFO::Done
2024-06-10 00:50:28.006632 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:50:28.009519 INFO::Starting hierarchical adjustment
2024-06-10 00:50:28.010719 INFO::Found 2 batches.
2024-06-10 00:50:28.011812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:50:28.012918 INFO::Using default BPPARAM
2024-06-10 00:50:28.01392 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:50:28.015614 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:50:28.033788 INFO::Done
2024-06-10 00:50:28.034676 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:50:28.037014 INFO::ASW Batch was -0.0517294030730504 prior to batch effect correction and is now -0.116180348321492 .
2024-06-10 00:50:28.037993 INFO::Total function execution time is 0.0469901561737061 s and adjustment time is 0.0232408046722412 s ( 49.46 )
2024-06-10 00:50:28.040878 INFO::Formatting Data.
2024-06-10 00:50:28.041712 INFO::Replacing NaNs with NAs.
2024-06-10 00:50:28.048829 INFO::Formatting Data.
2024-06-10 00:50:28.049654 INFO::Replacing NaNs with NAs.
2024-06-10 00:50:28.050654 INFO::Removing potential empty rows and columns
2024-06-10 00:50:28.051749 INFO::Found 0 missing values.
2024-06-10 00:50:28.05415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:50:28.054861 INFO::Done
2024-06-10 00:50:28.057065 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:50:28.0592 INFO::Starting hierarchical adjustment
2024-06-10 00:50:28.060171 INFO::Found 2 batches.
2024-06-10 00:50:28.061281 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:50:28.062719 INFO::Using default BPPARAM
2024-06-10 00:50:28.065421 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:50:28.067126 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:50:28.083587 INFO::Done
2024-06-10 00:50:28.084456 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:50:28.086641 INFO::ASW Batch was -0.0194533429069141 prior to batch effect correction and is now -0.11841142560783 .
2024-06-10 00:50:28.088054 INFO::Total function execution time is 0.039168119430542 s and adjustment time is 0.0236179828643799 s ( 60.3 )
2024-06-10 00:50:28.089822 INFO::Formatting Data.
2024-06-10 00:50:28.090829 INFO::Replacing NaNs with NAs.
2024-06-10 00:50:28.091847 INFO::Removing potential empty rows and columns
2024-06-10 00:50:28.093018 INFO::Found 0 missing values.
2024-06-10 00:50:28.09546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:50:28.096236 INFO::Done
2024-06-10 00:50:28.096938 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:50:28.098953 INFO::Starting hierarchical adjustment
2024-06-10 00:50:28.09981 INFO::Found 2 batches.
2024-06-10 00:50:28.100609 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:50:28.101707 INFO::Using default BPPARAM
2024-06-10 00:50:28.102424 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:50:28.103466 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:50:28.116393 INFO::Done
2024-06-10 00:50:28.117244 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:50:28.119367 INFO::ASW Batch was -0.0194533429069141 prior to batch effect correction and is now -0.11841142560783 .
2024-06-10 00:50:28.120331 INFO::Total function execution time is 0.0305778980255127 s and adjustment time is 0.0166862010955811 s ( 54.57 )
2024-06-10 00:50:30.590231 INFO::Formatting Data.
2024-06-10 00:50:30.591174 INFO::Recognized SummarizedExperiment
2024-06-10 00:50:30.591912 INFO::Typecasting input to dataframe.
2024-06-10 00:50:30.655627 INFO::Replacing NaNs with NAs.
2024-06-10 00:50:30.657885 INFO::Removing potential empty rows and columns
2024-06-10 00:50:30.662949 INFO::Found 0 missing values.
2024-06-10 00:50:31.47433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:50:31.475852 INFO::Done
2024-06-10 00:50:31.477176 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:50:31.483276 INFO::Starting hierarchical adjustment
2024-06-10 00:50:31.48475 INFO::Found 2 batches.
2024-06-10 00:50:31.487627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:50:31.48954 INFO::Using default BPPARAM
2024-06-10 00:50:31.490715 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:50:31.492617 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:50:31.550553 INFO::Done
2024-06-10 00:50:31.551413 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:50:31.55507 INFO::ASW Batch was -0.0115423430532587 prior to batch effect correction and is now -0.0887868551027836 .
2024-06-10 00:50:31.55642 INFO::Total function execution time is 0.966416120529175 s and adjustment time is 0.0660359859466553 s ( 6.83 )
2024-06-10 00:50:31.585367 INFO::Formatting Data.
2024-06-10 00:50:31.586824 INFO::Recognized SummarizedExperiment
2024-06-10 00:50:31.588069 INFO::Typecasting input to dataframe.
2024-06-10 00:50:31.60189 INFO::Replacing NaNs with NAs.
2024-06-10 00:50:31.60415 INFO::Removing potential empty rows and columns
2024-06-10 00:50:31.609139 INFO::Found 0 missing values.
2024-06-10 00:50:31.618531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:50:31.619933 INFO::Done
2024-06-10 00:50:31.621189 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:50:31.627334 INFO::Starting hierarchical adjustment
2024-06-10 00:50:31.629022 INFO::Found 2 batches.
2024-06-10 00:50:31.630273 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:50:31.631611 INFO::Using default BPPARAM
2024-06-10 00:50:31.632825 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:50:31.634993 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:50:31.667715 INFO::Done
2024-06-10 00:50:31.669108 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:50:31.675336 INFO::ASW Batch was -0.00615221196215545 prior to batch effect correction and is now -0.00615221196215545 .
2024-06-10 00:50:31.676808 INFO::Total function execution time is 0.0914230346679688 s and adjustment time is 0.038884162902832 s ( 42.53 )
2024-06-10 00:50:31.710627 INFO::Formatting Data.
2024-06-10 00:50:31.712147 INFO::Replacing NaNs with NAs.
2024-06-10 00:50:31.713595 INFO::Removing potential empty rows and columns
2024-06-10 00:50:31.715458 INFO::Found 0 missing values.
2024-06-10 00:50:31.720044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:50:31.721412 INFO::Done
2024-06-10 00:50:31.722639 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:50:31.72603 INFO::Starting hierarchical adjustment
2024-06-10 00:50:31.727471 INFO::Found 3 batches.
2024-06-10 00:50:31.728671 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:50:31.729939 INFO::Using default BPPARAM
2024-06-10 00:50:31.731143 INFO::Processing subtree level 1
2024-06-10 00:50:54.035633 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:50:54.037883 INFO::Done
2024-06-10 00:50:54.039175 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:50:54.042206 INFO::ASW Batch was -0.0786428713438047 prior to batch effect correction and is now -0.151846625443365 .
2024-06-10 00:50:54.043651 INFO::Total function execution time is 22.3331341743469 s and adjustment time is 22.3105981349945 s ( 99.9 )
2024-06-10 00:50:54.066755 INFO::Skipping initial DF formatting
2024-06-10 00:50:54.068046 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:50:54.07411 INFO::Starting hierarchical adjustment
2024-06-10 00:50:54.075507 INFO::Found 5 batches.
2024-06-10 00:50:54.0766 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:50:54.077741 INFO::Using default BPPARAM
2024-06-10 00:50:54.078813 INFO::Processing subtree level 1
2024-06-10 00:51:07.662694 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:51:07.664708 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:51:07.686494 INFO::Done
2024-06-10 00:51:07.687797 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:51:07.692032 INFO::ASW Batch was 0.496963325295293 prior to batch effect correction and is now 0.496963325295293 .
2024-06-10 00:51:07.692892 INFO::ASW Label was 0.379085504174825 prior to batch effect correction and is now 0.379085504174825 .
2024-06-10 00:51:07.693875 INFO::Total function execution time is 13.6272809505463 s and adjustment time is 13.6111600399017 s ( 99.88 )
2024-06-10 00:51:07.720811 INFO::Formatting Data.
2024-06-10 00:51:07.722347 INFO::Replacing NaNs with NAs.
2024-06-10 00:51:07.723546 INFO::Removing potential empty rows and columns
2024-06-10 00:51:07.724643 INFO::Found 0 missing values.
2024-06-10 00:51:07.728079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:51:07.728804 INFO::Done
2024-06-10 00:51:07.729509 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:51:07.732496 INFO::Starting hierarchical adjustment
2024-06-10 00:51:07.733362 INFO::Found 5 batches.
2024-06-10 00:51:07.734061 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:51:07.734822 INFO::Using default BPPARAM
2024-06-10 00:51:07.735528 INFO::Processing subtree level 1
2024-06-10 00:51:21.353529 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:51:21.354974 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:51:21.372942 INFO::Done
2024-06-10 00:51:21.374415 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:51:21.379121 INFO::ASW Batch was 0.54645479352383 prior to batch effect correction and is now -0.085085640155278 .
2024-06-10 00:51:21.380513 INFO::ASW Label was 0.247095148468489 prior to batch effect correction and is now 0.782322730717525 .
2024-06-10 00:51:21.382083 INFO::Total function execution time is 13.6613850593567 s and adjustment time is 13.639622926712 s ( 99.84 )
2024-06-10 00:51:21.383704 INFO::Formatting Data.
2024-06-10 00:51:21.385024 INFO::Replacing NaNs with NAs.
2024-06-10 00:51:21.38675 INFO::Removing potential empty rows and columns
2024-06-10 00:51:21.388556 INFO::Found 0 missing values.
2024-06-10 00:51:21.394255 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:51:21.395583 INFO::Done
2024-06-10 00:51:21.396801 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:51:21.401494 INFO::Starting hierarchical adjustment
2024-06-10 00:51:21.402822 INFO::Found 5 batches.
2024-06-10 00:51:21.40388 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:51:21.405035 INFO::Using default BPPARAM
2024-06-10 00:51:21.406081 INFO::Processing subtree level 1
2024-06-10 00:51:34.834055 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:51:34.835848 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:51:34.852975 INFO::Done
2024-06-10 00:51:34.854356 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:51:34.858846 INFO::ASW Batch was 0.54645479352383 prior to batch effect correction and is now -0.085085640155278 .
2024-06-10 00:51:34.860008 INFO::ASW Label was 0.247095148468489 prior to batch effect correction and is now 0.782322730717525 .
2024-06-10 00:51:34.861358 INFO::Total function execution time is 13.4776759147644 s and adjustment time is 13.4503209590912 s ( 99.8 )
2024-06-10 00:51:34.88234 INFO::Formatting Data.
2024-06-10 00:51:34.883842 INFO::Replacing NaNs with NAs.
2024-06-10 00:51:34.885038 INFO::Removing potential empty rows and columns
2024-06-10 00:51:34.886161 INFO::Found 0 missing values.
2024-06-10 00:51:34.889568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:51:34.890294 INFO::Done
2024-06-10 00:51:34.890994 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:51:34.893958 INFO::Starting hierarchical adjustment
2024-06-10 00:51:34.894842 INFO::Found 5 batches.
2024-06-10 00:51:34.895552 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:51:34.896357 INFO::Using default BPPARAM
2024-06-10 00:51:34.897075 INFO::Processing subtree level 1
2024-06-10 00:51:48.022567 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:51:48.024731 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:51:48.043359 INFO::Done
2024-06-10 00:51:48.04478 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:51:48.04954 INFO::ASW Batch was 0.367856036886968 prior to batch effect correction and is now -0.0600807634967946 .
2024-06-10 00:51:48.050911 INFO::ASW Label was 0.326021934184907 prior to batch effect correction and is now 0.804339776730443 .
2024-06-10 00:51:48.052499 INFO::Total function execution time is 13.1702477931976 s and adjustment time is 13.1485719680786 s ( 99.84 )
2024-06-10 00:51:48.054024 INFO::Formatting Data.
2024-06-10 00:51:48.055348 INFO::Replacing NaNs with NAs.
2024-06-10 00:51:48.057044 INFO::Removing potential empty rows and columns
2024-06-10 00:51:48.058519 INFO::Found 0 missing values.
2024-06-10 00:51:48.063494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:51:48.064342 INFO::Done
2024-06-10 00:51:48.065065 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:51:48.067946 INFO::Starting hierarchical adjustment
2024-06-10 00:51:48.068818 INFO::Found 5 batches.
2024-06-10 00:51:48.06952 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:51:48.070375 INFO::Using default BPPARAM
2024-06-10 00:51:48.07157 INFO::Processing subtree level 1
2024-06-10 00:52:01.542942 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:52:01.545014 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:52:01.557052 INFO::Done
2024-06-10 00:52:01.557975 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:52:01.560983 INFO::ASW Batch was 0.367856036886968 prior to batch effect correction and is now -0.0600807634967946 .
2024-06-10 00:52:01.561806 INFO::ASW Label was 0.326021934184907 prior to batch effect correction and is now 0.804339776730443 .
2024-06-10 00:52:01.562766 INFO::Total function execution time is 13.5088469982147 s and adjustment time is 13.4883329868317 s ( 99.85 )
2024-06-10 00:52:01.579204 INFO::Formatting Data.
2024-06-10 00:52:01.580156 INFO::Replacing NaNs with NAs.
2024-06-10 00:52:01.581212 INFO::Removing potential empty rows and columns
2024-06-10 00:52:01.582315 INFO::Found 0 missing values.
2024-06-10 00:52:01.584675 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:52:01.58539 INFO::Done
2024-06-10 00:52:01.586078 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:52:01.588941 INFO::Starting hierarchical adjustment
2024-06-10 00:52:01.589802 INFO::Found 2 batches.
2024-06-10 00:52:01.590499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:52:01.591258 INFO::Using default BPPARAM
2024-06-10 00:52:01.591957 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:52:01.592995 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:52:01.604362 INFO::Done
2024-06-10 00:52:01.605196 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:52:01.608068 INFO::ASW Batch was 0.563230606901662 prior to batch effect correction and is now -0.0246370025966862 .
2024-06-10 00:52:01.608819 INFO::ASW Label was 0.533357858258069 prior to batch effect correction and is now 0.917951247590329 .
2024-06-10 00:52:01.609739 INFO::Total function execution time is 0.0306310653686523 s and adjustment time is 0.0146839618682861 s ( 47.94 )
2024-06-10 00:52:01.610656 INFO::Formatting Data.
2024-06-10 00:52:01.611442 INFO::Replacing NaNs with NAs.
2024-06-10 00:52:01.6125 INFO::Removing potential empty rows and columns
2024-06-10 00:52:01.613562 INFO::Found 0 missing values.
2024-06-10 00:52:01.615871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:52:01.616587 INFO::Done
2024-06-10 00:52:01.617316 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:52:01.620242 INFO::Starting hierarchical adjustment
2024-06-10 00:52:01.621104 INFO::Found 2 batches.
2024-06-10 00:52:01.621834 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:52:01.622624 INFO::Using default BPPARAM
2024-06-10 00:52:01.623319 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:52:01.624376 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:52:01.636759 INFO::Done
2024-06-10 00:52:01.637723 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:52:01.641147 INFO::ASW Batch was 0.563230606901662 prior to batch effect correction and is now -0.0246370025966862 .
2024-06-10 00:52:01.641925 INFO::ASW Label was 0.533357858258069 prior to batch effect correction and is now 0.917951247590329 .
2024-06-10 00:52:01.642868 INFO::Total function execution time is 0.0322170257568359 s and adjustment time is 0.0157570838928223 s ( 48.91 )
2024-06-10 00:52:01.658536 INFO::Formatting Data.
2024-06-10 00:52:01.659561 INFO::Replacing NaNs with NAs.
2024-06-10 00:52:01.660696 INFO::Removing potential empty rows and columns
2024-06-10 00:52:01.661749 INFO::Found 0 missing values.
2024-06-10 00:52:01.663789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:52:01.66456 INFO::Done
2024-06-10 00:52:01.665259 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:52:01.667227 INFO::Starting hierarchical adjustment
2024-06-10 00:52:01.66808 INFO::Found 2 batches.
2024-06-10 00:52:01.668777 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:52:01.669598 INFO::Using default BPPARAM
2024-06-10 00:52:01.670301 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:52:01.67135 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:52:01.695941 INFO::Done
2024-06-10 00:52:01.696818 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:52:01.698801 INFO::ASW Batch was 0.259158430100384 prior to batch effect correction and is now -0.164935553651512 .
2024-06-10 00:52:01.699768 INFO::Total function execution time is 0.0413789749145508 s and adjustment time is 0.0279500484466553 s ( 67.55 )
2024-06-10 00:52:01.715145 INFO::Formatting Data.
2024-06-10 00:52:01.716097 INFO::Replacing NaNs with NAs.
2024-06-10 00:52:01.717184 INFO::Removing potential empty rows and columns
2024-06-10 00:52:01.718368 INFO::Found 0 missing values.
2024-06-10 00:52:01.719761 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.
2024-06-10 00:52:01.725857 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:52:01.727144 INFO::Done
2024-06-10 00:52:01.728365 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:52:01.733 INFO::Starting hierarchical adjustment
2024-06-10 00:52:01.734492 INFO::Found 2 batches.
2024-06-10 00:52:01.735632 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:52:01.736756 INFO::Using default BPPARAM
2024-06-10 00:52:01.737761 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:52:01.739292 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:52:01.759472 INFO::Done
2024-06-10 00:52:01.76069 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:52:01.764947 INFO::ASW Batch was 0.349497690571848 prior to batch effect correction and is now -0.021150981916413 .
2024-06-10 00:52:01.766078 INFO::ASW Label was 0.719832171374791 prior to batch effect correction and is now 0.937290081827582 .
2024-06-10 00:52:01.767441 INFO::Total function execution time is 0.0523138046264648 s and adjustment time is 0.025184154510498 s ( 48.14 )
2024-06-10 00:52:01.768762 INFO::Formatting Data.
2024-06-10 00:52:01.769886 INFO::Replacing NaNs with NAs.
2024-06-10 00:52:01.771382 INFO::Removing potential empty rows and columns
2024-06-10 00:52:01.772961 INFO::Found 0 missing values.
2024-06-10 00:52:01.774498 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.
2024-06-10 00:52:01.780534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:52:01.781648 INFO::Done
2024-06-10 00:52:01.7827 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:52:01.787343 INFO::Starting hierarchical adjustment
2024-06-10 00:52:01.788787 INFO::Found 2 batches.
2024-06-10 00:52:01.789985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:52:01.791265 INFO::Using default BPPARAM
2024-06-10 00:52:01.792431 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:52:01.79415 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:52:01.817918 INFO::Done
2024-06-10 00:52:01.819296 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:52:01.824018 INFO::ASW Batch was 0.349497690571848 prior to batch effect correction and is now -0.021150981916413 .
2024-06-10 00:52:01.825271 INFO::ASW Label was 0.719832171374791 prior to batch effect correction and is now 0.937290081827582 .
2024-06-10 00:52:01.826818 INFO::Total function execution time is 0.0580430030822754 s and adjustment time is 0.0292980670928955 s ( 50.48 )
2024-06-10 00:52:02.104215 INFO::Formatting Data.
2024-06-10 00:52:02.105674 INFO::Replacing NaNs with NAs.
2024-06-10 00:52:02.107332 INFO::Removing potential empty rows and columns
2024-06-10 00:52:02.109072 INFO::Found 0 missing values.
2024-06-10 00:52:02.114449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:52:02.115681 INFO::Done
2024-06-10 00:52:02.116812 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:52:02.120057 INFO::Starting hierarchical adjustment
2024-06-10 00:52:02.121759 INFO::Found 3 batches.
2024-06-10 00:52:02.122858 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:52:02.12407 INFO::Using default BPPARAM
2024-06-10 00:52:02.125181 INFO::Processing subtree level 1
2024-06-10 00:52:15.391427 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:52:15.393389 INFO::Done
2024-06-10 00:52:15.394708 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:52:15.397991 INFO::ASW Batch was -0.0355629872441912 prior to batch effect correction and is now -0.0355629872441912 .
2024-06-10 00:52:15.399481 INFO::Total function execution time is 13.2953779697418 s and adjustment time is 13.2718420028687 s ( 99.82 )
2024-06-10 00:52:15.401032 INFO::Formatting Data.
2024-06-10 00:52:15.402301 INFO::Typecasting input to dataframe.
2024-06-10 00:52:15.403594 INFO::Replacing NaNs with NAs.
2024-06-10 00:52:15.405121 INFO::Removing potential empty rows and columns
2024-06-10 00:52:15.406672 INFO::Found 0 missing values.
2024-06-10 00:52:15.410706 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:52:15.411734 INFO::Done
2024-06-10 00:52:15.412906 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:52:15.415886 INFO::Starting hierarchical adjustment
2024-06-10 00:52:15.41716 INFO::Found 3 batches.
2024-06-10 00:52:15.418156 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:52:15.41954 INFO::Using default BPPARAM
2024-06-10 00:52:15.420543 INFO::Processing subtree level 1
2024-06-10 00:52:28.771755 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:52:28.773969 INFO::Done
2024-06-10 00:52:28.775216 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:52:28.778256 INFO::ASW Batch was -0.0355629872441912 prior to batch effect correction and is now -0.0355629872441912 .
2024-06-10 00:52:28.779676 INFO::Total function execution time is 13.3786618709564 s and adjustment time is 13.3569750785828 s ( 99.84 )
2024-06-10 00:52:28.800055 INFO::Formatting Data.
2024-06-10 00:52:28.801097 INFO::Typecasting input to dataframe.
2024-06-10 00:52:28.802175 INFO::Replacing NaNs with NAs.
2024-06-10 00:52:28.803252 INFO::Removing potential empty rows and columns
2024-06-10 00:52:28.804468 INFO::Found 0 missing values.
2024-06-10 00:52:28.80721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:52:28.807993 INFO::Done
2024-06-10 00:52:28.8087 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:52:28.810724 INFO::Starting hierarchical adjustment
2024-06-10 00:52:28.811586 INFO::Found 3 batches.
2024-06-10 00:52:28.812281 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:52:28.81307 INFO::Using default BPPARAM
2024-06-10 00:52:28.813788 INFO::Processing subtree level 1
2024-06-10 00:52:42.215963 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:52:42.217982 INFO::Done
2024-06-10 00:52:42.219137 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:52:42.222109 INFO::ASW Batch was -0.0791746531032242 prior to batch effect correction and is now -0.0791746531032242 .
2024-06-10 00:52:42.223536 INFO::Total function execution time is 13.4234988689423 s and adjustment time is 13.4064750671387 s ( 99.87 )
2024-06-10 00:52:55.186942 INFO::Formatting Data.
2024-06-10 00:52:55.188504 INFO::Replacing NaNs with NAs.
2024-06-10 00:52:55.190632 INFO::Removing potential empty rows and columns
2024-06-10 00:52:55.195557 INFO::Found 1000 missing values.
2024-06-10 00:52:55.218541 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:52:55.219812 INFO::Done
2024-06-10 00:52:55.221043 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:52:55.231535 INFO::Starting hierarchical adjustment
2024-06-10 00:52:55.233187 INFO::Found 10 batches.
2024-06-10 00:52:55.234937 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:52:55.236123 INFO::Using default BPPARAM
2024-06-10 00:52:55.237185 INFO::Processing subtree level 1
2024-06-10 00:53:09.332618 INFO::Processing subtree level 2
2024-06-10 00:53:22.457322 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:53:22.459729 INFO::Done
2024-06-10 00:53:22.460974 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:53:22.469852 INFO::ASW Batch was 0.46160788588477 prior to batch effect correction and is now 0.46160788588477 .
2024-06-10 00:53:22.471422 INFO::ASW Label was 0.370442255723571 prior to batch effect correction and is now 0.370442255723571 .
2024-06-10 00:53:22.473015 INFO::Total function execution time is 27.2862019538879 s and adjustment time is 27.2268149852753 s ( 99.78 )
2024-06-10 00:53:22.474401 INFO::Formatting Data.
2024-06-10 00:53:22.475586 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:22.4775 INFO::Removing potential empty rows and columns
2024-06-10 00:53:22.480858 INFO::Found 1000 missing values.
2024-06-10 00:53:22.494224 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:22.49518 INFO::Done
2024-06-10 00:53:22.495955 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:53:22.502135 INFO::Starting hierarchical adjustment
2024-06-10 00:53:22.503094 INFO::Found 10 batches.
2024-06-10 00:53:23.184878 INFO::Set up parallel execution backend with 2 workers
2024-06-10 00:53:23.186362 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-10 00:53:31.638002 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:53:31.639616 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:53:31.654362 INFO::Done
2024-06-10 00:53:31.655262 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:53:31.661146 INFO::ASW Batch was 0.46160788588477 prior to batch effect correction and is now 0.46160788588477 .
2024-06-10 00:53:31.661988 INFO::ASW Label was 0.370442255723571 prior to batch effect correction and is now 0.370442255723571 .
2024-06-10 00:53:31.663054 INFO::Total function execution time is 9.18870997428894 s and adjustment time is 9.15137600898743 s ( 99.59 )
2024-06-10 00:53:44.867281 INFO::Formatting Data.
2024-06-10 00:53:44.868811 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:44.870625 INFO::Removing potential empty rows and columns
2024-06-10 00:53:44.872503 INFO::Found 0 missing values.
2024-06-10 00:53:44.878102 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:44.879338 INFO::Done
2024-06-10 00:53:44.880637 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:53:44.885003 INFO::Starting hierarchical adjustment
2024-06-10 00:53:44.886403 INFO::Found 3 batches.
2024-06-10 00:53:44.887581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:53:44.888715 INFO::Using default BPPARAM
2024-06-10 00:53:44.889733 INFO::Processing subtree level 1
2024-06-10 00:53:57.826482 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:53:57.828776 INFO::Done
2024-06-10 00:53:57.830045 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:53:57.834132 INFO::ASW Batch was 0.163547603794042 prior to batch effect correction and is now -0.130374810847391 .
2024-06-10 00:53:57.835321 INFO::ASW Label was -0.186811620715022 prior to batch effect correction and is now -0.018254809507405 .
2024-06-10 00:53:57.836746 INFO::Total function execution time is 12.9695899486542 s and adjustment time is 12.9425628185272 s ( 99.79 )
2024-06-10 00:53:57.988688 INFO::Formatting Data.
2024-06-10 00:53:57.990047 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:57.991637 INFO::Removing potential empty rows and columns
2024-06-10 00:53:57.993386 INFO::Found 2 missing values.
2024-06-10 00:53:57.997279 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:57.998357 INFO::Done
2024-06-10 00:53:58.055102 INFO::Found NA in Reference column
2024-06-10 00:53:58.073911 INFO::Require at least two references per batch.
2024-06-10 00:53:58.098728 INFO::Formatting Data.
2024-06-10 00:53:58.100007 INFO::Recognized SummarizedExperiment
2024-06-10 00:53:58.101088 INFO::Typecasting input to dataframe.
2024-06-10 00:53:58.112657 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:58.114499 INFO::Removing potential empty rows and columns
2024-06-10 00:53:58.118963 INFO::Found 0 missing values.
2024-06-10 00:53:58.127556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:58.128771 INFO::Done
2024-06-10 00:53:58.150547 INFO::Formatting Data.
2024-06-10 00:53:58.151859 INFO::Recognized SummarizedExperiment
2024-06-10 00:53:58.15296 INFO::Typecasting input to dataframe.
2024-06-10 00:53:58.175446 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:58.177389 INFO::Removing potential empty rows and columns
2024-06-10 00:53:58.182016 INFO::Found 0 missing values.
2024-06-10 00:53:58.194665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:58.196119 INFO::Done
2024-06-10 00:53:58.21899 INFO::Formatting Data.
2024-06-10 00:53:58.220444 INFO::Recognized SummarizedExperiment
2024-06-10 00:53:58.221754 INFO::Typecasting input to dataframe.
2024-06-10 00:53:58.243954 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:58.245686 INFO::Removing potential empty rows and columns
2024-06-10 00:53:58.247542 INFO::Found 0 missing values.
2024-06-10 00:53:58.24916 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.
2024-06-10 00:53:58.254979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:58.256069 INFO::Done
2024-06-10 00:53:58.275904 INFO::Formatting Data.
2024-06-10 00:53:58.277509 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:58.279226 INFO::Removing potential empty rows and columns
2024-06-10 00:53:58.280927 INFO::Found 0 missing values.
2024-06-10 00:53:58.284925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:58.28599 INFO::Done
2024-06-10 00:53:58.31349 INFO::Formatting Data.
2024-06-10 00:53:58.314892 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:58.316415 INFO::Removing potential empty rows and columns
2024-06-10 00:53:58.318046 INFO::Found 0 missing values.
2024-06-10 00:53:58.322128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:58.323222 INFO::Done
2024-06-10 00:53:58.376573 INFO::Formatting Data.
2024-06-10 00:53:58.377576 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:58.378753 INFO::Removing potential empty rows and columns
2024-06-10 00:53:58.379973 INFO::Found 1 missing values.
2024-06-10 00:53:58.382402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:58.383142 INFO::Done
2024-06-10 00:53:58.408392 INFO::Formatting Data.
2024-06-10 00:53:58.409913 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:58.411599 INFO::Removing potential empty rows and columns
2024-06-10 00:53:58.413402 INFO::Found 2 missing values.
2024-06-10 00:53:58.415083 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.
2024-06-10 00:53:58.418631 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:58.419829 INFO::Done
2024-06-10 00:53:58.437259 INFO::Formatting Data.
2024-06-10 00:53:58.438264 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:58.439325 INFO::Removing potential empty rows and columns
2024-06-10 00:53:58.440385 INFO::Found 2 missing values.
2024-06-10 00:53:58.442013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:58.442744 INFO::Done
2024-06-10 00:53:58.462493 INFO::Formatting Data.
2024-06-10 00:53:58.463841 INFO::Typecasting input to dataframe.
2024-06-10 00:53:58.465342 INFO::Replacing NaNs with NAs.
2024-06-10 00:53:58.466822 INFO::Removing potential empty rows and columns
2024-06-10 00:53:58.468434 INFO::Found 0 missing values.
2024-06-10 00:53:58.472382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:53:58.473414 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
27.87 11.42 260.25
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 7.83 | 4.69 | 28.45 | |
| compute_asw | 0.03 | 0.00 | 0.03 | |
| count_existing | 0 | 0 | 0 | |
| generate_data_covariables | 0.01 | 0.00 | 0.02 | |
| generate_dataset | 0.00 | 0.01 | 0.02 | |