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 14:43 -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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-06-10 08:21:22 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 08:23:35 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 133.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* 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 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 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 32.301 1.306 34.022
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 08:23:02.690977 INFO::Formatting Data.
2024-06-10 08:23:02.699513 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:02.71991 INFO::Removing potential empty rows and columns
2024-06-10 08:23:03.124702 INFO::Found 0 missing values.
2024-06-10 08:23:03.131643 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:03.132996 INFO::Done
2024-06-10 08:23:03.133662 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:03.165425 INFO::Starting hierarchical adjustment
2024-06-10 08:23:03.166455 INFO::Found 3 batches.
2024-06-10 08:23:03.166968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:03.168246 INFO::Using default BPPARAM
2024-06-10 08:23:03.168913 INFO::Processing subtree level 1
2024-06-10 08:23:03.395223 INFO::Adjusting the last 1 batches sequentially
2024-06-10 08:23:03.402722 INFO::Done
2024-06-10 08:23:03.404161 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:03.412707 INFO::ASW Batch was 0.00558233541485419 prior to batch effect correction and is now 0.00558233541485419 .
2024-06-10 08:23:03.418294 INFO::Total function execution time is 0.72819709777832 s and adjustment time is 0.236365795135498 s ( 32.46 )
2024-06-10 08:23:03.455856 INFO::Formatting Data.
2024-06-10 08:23:03.456867 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:03.458015 INFO::Removing potential empty rows and columns
2024-06-10 08:23:03.460774 INFO::Found 0 missing values.
2024-06-10 08:23:03.462214 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 08:23:03.48214 INFO::Formatting Data.
2024-06-10 08:23:03.486586 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:03.488192 INFO::Removing potential empty rows and columns
2024-06-10 08:23:03.489417 INFO::Found 0 missing values.
2024-06-10 08:23:03.492524 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 08:23:03.527917 INFO::Formatting Data.
2024-06-10 08:23:03.528977 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:03.529926 INFO::Removing potential empty rows and columns
2024-06-10 08:23:03.531017 INFO::Found 0 missing values.
2024-06-10 08:23:03.534026 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 08:23:03.538419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:03.539147 INFO::Done
2024-06-10 08:23:03.539586 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:03.544103 INFO::Starting hierarchical adjustment
2024-06-10 08:23:03.547726 INFO::Found 2 batches.
2024-06-10 08:23:03.548863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:03.549542 INFO::Using default BPPARAM
2024-06-10 08:23:03.550036 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:03.55106 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:03.601078 INFO::Done
2024-06-10 08:23:03.60614 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:03.608959 INFO::ASW Batch was -0.0196175511269121 prior to batch effect correction and is now -0.122895752592307 .
2024-06-10 08:23:03.612398 INFO::Total function execution time is 0.0853030681610107 s and adjustment time is 0.0559878349304199 s ( 65.63 )
2024-06-10 08:23:03.619005 INFO::Formatting Data.
2024-06-10 08:23:03.619921 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:03.634043 INFO::Formatting Data.
2024-06-10 08:23:03.634891 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:03.638789 INFO::Removing potential empty rows and columns
2024-06-10 08:23:03.639951 INFO::Found 0 missing values.
2024-06-10 08:23:03.64458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:03.645446 INFO::Done
2024-06-10 08:23:03.645908 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:03.651764 INFO::Starting hierarchical adjustment
2024-06-10 08:23:03.652742 INFO::Found 2 batches.
2024-06-10 08:23:03.653213 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:03.653709 INFO::Using default BPPARAM
2024-06-10 08:23:03.654097 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:03.65639 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:03.684707 INFO::Done
2024-06-10 08:23:03.685555 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:03.690727 INFO::ASW Batch was -0.0248363862726955 prior to batch effect correction and is now -0.116399089994285 .
2024-06-10 08:23:03.69189 INFO::Total function execution time is 0.0579540729522705 s and adjustment time is 0.0320529937744141 s ( 55.31 )
2024-06-10 08:23:03.692936 INFO::Formatting Data.
2024-06-10 08:23:03.695257 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:03.696453 INFO::Removing potential empty rows and columns
2024-06-10 08:23:03.697402 INFO::Found 0 missing values.
2024-06-10 08:23:03.703886 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:03.704662 INFO::Done
2024-06-10 08:23:03.705095 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:03.70858 INFO::Starting hierarchical adjustment
2024-06-10 08:23:03.709454 INFO::Found 2 batches.
2024-06-10 08:23:03.709872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:03.710451 INFO::Using default BPPARAM
2024-06-10 08:23:03.7109 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:03.715926 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:03.736881 INFO::Done
2024-06-10 08:23:03.737651 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:03.739521 INFO::ASW Batch was -0.0248363862726955 prior to batch effect correction and is now -0.116399089994285 .
2024-06-10 08:23:03.740375 INFO::Total function execution time is 0.047421932220459 s and adjustment time is 0.0275180339813232 s ( 58.03 )
2024-06-10 08:23:06.993335 INFO::Formatting Data.
2024-06-10 08:23:06.994487 INFO::Recognized SummarizedExperiment
2024-06-10 08:23:06.994979 INFO::Typecasting input to dataframe.
2024-06-10 08:23:08.452509 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:08.454054 INFO::Removing potential empty rows and columns
2024-06-10 08:23:08.457274 INFO::Found 0 missing values.
2024-06-10 08:23:08.46356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:08.464281 INFO::Done
2024-06-10 08:23:08.464683 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:08.468071 INFO::Starting hierarchical adjustment
2024-06-10 08:23:08.468894 INFO::Found 2 batches.
2024-06-10 08:23:08.469294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:08.470261 INFO::Using default BPPARAM
2024-06-10 08:23:08.470693 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:08.471575 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:08.520769 INFO::Done
2024-06-10 08:23:08.521587 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:08.524949 INFO::ASW Batch was -0.00145544903929704 prior to batch effect correction and is now -0.09237332820054 .
2024-06-10 08:23:08.526001 INFO::Total function execution time is 1.53329801559448 s and adjustment time is 0.0519430637359619 s ( 3.39 )
2024-06-10 08:23:08.562696 INFO::Formatting Data.
2024-06-10 08:23:08.564873 INFO::Recognized SummarizedExperiment
2024-06-10 08:23:08.565626 INFO::Typecasting input to dataframe.
2024-06-10 08:23:08.586024 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:08.587527 INFO::Removing potential empty rows and columns
2024-06-10 08:23:08.593537 INFO::Found 0 missing values.
2024-06-10 08:23:08.606435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:08.607294 INFO::Done
2024-06-10 08:23:08.607816 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:08.617818 INFO::Starting hierarchical adjustment
2024-06-10 08:23:08.618796 INFO::Found 2 batches.
2024-06-10 08:23:08.619221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:08.619681 INFO::Using default BPPARAM
2024-06-10 08:23:08.620036 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:08.622011 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:08.655688 INFO::Done
2024-06-10 08:23:08.656439 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:08.660562 INFO::ASW Batch was -0.0237036126782835 prior to batch effect correction and is now -0.0237036126782835 .
2024-06-10 08:23:08.664201 INFO::Total function execution time is 0.0989570617675781 s and adjustment time is 0.0369851589202881 s ( 37.37 )
2024-06-10 08:23:08.694137 INFO::Formatting Data.
2024-06-10 08:23:08.694892 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:08.695585 INFO::Removing potential empty rows and columns
2024-06-10 08:23:08.696395 INFO::Found 0 missing values.
2024-06-10 08:23:08.698629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:08.699138 INFO::Done
2024-06-10 08:23:08.699501 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:08.701251 INFO::Starting hierarchical adjustment
2024-06-10 08:23:08.701861 INFO::Found 3 batches.
2024-06-10 08:23:08.702225 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:08.702679 INFO::Using default BPPARAM
2024-06-10 08:23:08.703014 INFO::Processing subtree level 1
2024-06-10 08:23:09.003426 INFO::Adjusting the last 1 batches sequentially
2024-06-10 08:23:09.014371 INFO::Done
2024-06-10 08:23:09.016622 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:09.023254 INFO::ASW Batch was -0.0845253683265207 prior to batch effect correction and is now -0.152917262544251 .
2024-06-10 08:23:09.027843 INFO::Total function execution time is 0.333472967147827 s and adjustment time is 0.312422037124634 s ( 93.69 )
2024-06-10 08:23:09.067423 INFO::Skipping initial DF formatting
2024-06-10 08:23:09.068365 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:09.074012 INFO::Starting hierarchical adjustment
2024-06-10 08:23:09.07561 INFO::Found 5 batches.
2024-06-10 08:23:09.080262 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:09.081188 INFO::Using default BPPARAM
2024-06-10 08:23:09.081682 INFO::Processing subtree level 1
2024-06-10 08:23:09.337914 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:09.344539 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:09.406536 INFO::Done
2024-06-10 08:23:09.407672 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:09.414572 INFO::ASW Batch was 0.50708209297907 prior to batch effect correction and is now 0.50708209297907 .
2024-06-10 08:23:09.419191 INFO::ASW Label was 0.369290374433498 prior to batch effect correction and is now 0.369290374433498 .
2024-06-10 08:23:09.420406 INFO::Total function execution time is 0.353080034255981 s and adjustment time is 0.33110785484314 s ( 93.78 )
2024-06-10 08:23:09.461111 INFO::Formatting Data.
2024-06-10 08:23:09.462437 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:09.463788 INFO::Removing potential empty rows and columns
2024-06-10 08:23:09.465254 INFO::Found 0 missing values.
2024-06-10 08:23:09.469366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:09.470177 INFO::Done
2024-06-10 08:23:09.470648 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:09.473946 INFO::Starting hierarchical adjustment
2024-06-10 08:23:09.474909 INFO::Found 5 batches.
2024-06-10 08:23:09.475405 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:09.475982 INFO::Using default BPPARAM
2024-06-10 08:23:09.476412 INFO::Processing subtree level 1
2024-06-10 08:23:09.676714 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:09.689399 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:09.741707 INFO::Done
2024-06-10 08:23:09.743037 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:09.750336 INFO::ASW Batch was 0.244597035647783 prior to batch effect correction and is now 0.0420381112037292 .
2024-06-10 08:23:09.75374 INFO::ASW Label was 0.327468373942135 prior to batch effect correction and is now 0.669985785016454 .
2024-06-10 08:23:09.754975 INFO::Total function execution time is 0.294054985046387 s and adjustment time is 0.266827821731567 s ( 90.74 )
2024-06-10 08:23:09.756429 INFO::Formatting Data.
2024-06-10 08:23:09.760457 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:09.76229 INFO::Removing potential empty rows and columns
2024-06-10 08:23:09.765757 INFO::Found 0 missing values.
2024-06-10 08:23:09.774801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:09.775727 INFO::Done
2024-06-10 08:23:09.776332 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:09.782057 INFO::Starting hierarchical adjustment
2024-06-10 08:23:09.78325 INFO::Found 5 batches.
2024-06-10 08:23:09.786527 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:09.787333 INFO::Using default BPPARAM
2024-06-10 08:23:09.78794 INFO::Processing subtree level 1
2024-06-10 08:23:09.99655 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:10.007807 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:10.045005 INFO::Done
2024-06-10 08:23:10.046278 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:10.05651 INFO::ASW Batch was 0.244597035647783 prior to batch effect correction and is now 0.0420381112037292 .
2024-06-10 08:23:10.057367 INFO::ASW Label was 0.327468373942135 prior to batch effect correction and is now 0.669985785016454 .
2024-06-10 08:23:10.058205 INFO::Total function execution time is 0.301882982254028 s and adjustment time is 0.261904954910278 s ( 86.76 )
2024-06-10 08:23:10.09556 INFO::Formatting Data.
2024-06-10 08:23:10.096645 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:10.100779 INFO::Removing potential empty rows and columns
2024-06-10 08:23:10.102679 INFO::Found 0 missing values.
2024-06-10 08:23:10.106792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:10.107493 INFO::Done
2024-06-10 08:23:10.107942 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:10.111058 INFO::Starting hierarchical adjustment
2024-06-10 08:23:10.111944 INFO::Found 5 batches.
2024-06-10 08:23:10.112383 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:10.112973 INFO::Using default BPPARAM
2024-06-10 08:23:10.113396 INFO::Processing subtree level 1
2024-06-10 08:23:10.312114 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:10.322362 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:10.361618 INFO::Done
2024-06-10 08:23:10.363075 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:10.368856 INFO::ASW Batch was 0.516312275241108 prior to batch effect correction and is now -0.0510339748587619 .
2024-06-10 08:23:10.369707 INFO::ASW Label was 0.318407162906299 prior to batch effect correction and is now 0.747092228845059 .
2024-06-10 08:23:10.373728 INFO::Total function execution time is 0.275234937667847 s and adjustment time is 0.249737977981567 s ( 90.74 )
2024-06-10 08:23:10.375609 INFO::Formatting Data.
2024-06-10 08:23:10.376319 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:10.381108 INFO::Removing potential empty rows and columns
2024-06-10 08:23:10.382504 INFO::Found 0 missing values.
2024-06-10 08:23:10.389772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:10.39056 INFO::Done
2024-06-10 08:23:10.391036 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:10.396727 INFO::Starting hierarchical adjustment
2024-06-10 08:23:10.397652 INFO::Found 5 batches.
2024-06-10 08:23:10.398108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:10.402344 INFO::Using default BPPARAM
2024-06-10 08:23:10.402912 INFO::Processing subtree level 1
2024-06-10 08:23:10.600897 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:10.617804 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:10.668543 INFO::Done
2024-06-10 08:23:10.67198 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:10.679708 INFO::ASW Batch was 0.516312275241108 prior to batch effect correction and is now -0.0510339748587619 .
2024-06-10 08:23:10.680588 INFO::ASW Label was 0.318407162906299 prior to batch effect correction and is now 0.747092228845059 .
2024-06-10 08:23:10.683873 INFO::Total function execution time is 0.30588698387146 s and adjustment time is 0.270991086959839 s ( 88.59 )
2024-06-10 08:23:10.721855 INFO::Formatting Data.
2024-06-10 08:23:10.72282 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:10.723754 INFO::Removing potential empty rows and columns
2024-06-10 08:23:10.725712 INFO::Found 0 missing values.
2024-06-10 08:23:10.728574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:10.72919 INFO::Done
2024-06-10 08:23:10.733792 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:10.73774 INFO::Starting hierarchical adjustment
2024-06-10 08:23:10.738829 INFO::Found 2 batches.
2024-06-10 08:23:10.739293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:10.739842 INFO::Using default BPPARAM
2024-06-10 08:23:10.740223 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:10.741048 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:10.766995 INFO::Done
2024-06-10 08:23:10.770232 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:10.773422 INFO::ASW Batch was 0.676781614016337 prior to batch effect correction and is now 0.0077676909274923 .
2024-06-10 08:23:10.777894 INFO::ASW Label was 0.427941114894324 prior to batch effect correction and is now 0.930171821929662 .
2024-06-10 08:23:10.779224 INFO::Total function execution time is 0.0575001239776611 s and adjustment time is 0.0283408164978027 s ( 49.29 )
2024-06-10 08:23:10.779987 INFO::Formatting Data.
2024-06-10 08:23:10.780476 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:10.781349 INFO::Removing potential empty rows and columns
2024-06-10 08:23:10.786682 INFO::Found 0 missing values.
2024-06-10 08:23:10.789902 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:10.791735 INFO::Done
2024-06-10 08:23:10.792256 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:10.799557 INFO::Starting hierarchical adjustment
2024-06-10 08:23:10.800629 INFO::Found 2 batches.
2024-06-10 08:23:10.801098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:10.801588 INFO::Using default BPPARAM
2024-06-10 08:23:10.801979 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:10.805644 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:10.829281 INFO::Done
2024-06-10 08:23:10.839307 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:10.842022 INFO::ASW Batch was 0.676781614016337 prior to batch effect correction and is now 0.0077676909274923 .
2024-06-10 08:23:10.846518 INFO::ASW Label was 0.427941114894324 prior to batch effect correction and is now 0.930171821929662 .
2024-06-10 08:23:10.847442 INFO::Total function execution time is 0.0674259662628174 s and adjustment time is 0.0287790298461914 s ( 42.68 )
2024-06-10 08:23:10.872859 INFO::Formatting Data.
2024-06-10 08:23:10.873674 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:10.877127 INFO::Removing potential empty rows and columns
2024-06-10 08:23:10.878437 INFO::Found 0 missing values.
2024-06-10 08:23:10.880487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:10.883598 INFO::Done
2024-06-10 08:23:10.884153 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:10.886162 INFO::Starting hierarchical adjustment
2024-06-10 08:23:10.889917 INFO::Found 2 batches.
2024-06-10 08:23:10.890585 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:10.891119 INFO::Using default BPPARAM
2024-06-10 08:23:10.891516 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:10.892353 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:10.949845 INFO::Done
2024-06-10 08:23:10.950834 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:10.954698 INFO::ASW Batch was 0.434971484444843 prior to batch effect correction and is now -0.187116105191642 .
2024-06-10 08:23:10.95575 INFO::Total function execution time is 0.083172082901001 s and adjustment time is 0.0601420402526855 s ( 72.31 )
2024-06-10 08:23:10.984777 INFO::Formatting Data.
2024-06-10 08:23:10.985835 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:10.986763 INFO::Removing potential empty rows and columns
2024-06-10 08:23:10.98767 INFO::Found 0 missing values.
2024-06-10 08:23:10.992962 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 08:23:11.00224 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:11.003055 INFO::Done
2024-06-10 08:23:11.003496 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:11.010425 INFO::Starting hierarchical adjustment
2024-06-10 08:23:11.011395 INFO::Found 2 batches.
2024-06-10 08:23:11.014494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:11.015219 INFO::Using default BPPARAM
2024-06-10 08:23:11.015623 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:11.016923 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:11.051304 INFO::Done
2024-06-10 08:23:11.052153 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:11.057001 INFO::ASW Batch was 0.497829960046276 prior to batch effect correction and is now 0.0882226471362079 .
2024-06-10 08:23:11.057798 INFO::ASW Label was 0.554250149992516 prior to batch effect correction and is now 0.867731659794373 .
2024-06-10 08:23:11.058517 INFO::Total function execution time is 0.0739600658416748 s and adjustment time is 0.03997802734375 s ( 54.05 )
2024-06-10 08:23:11.05923 INFO::Formatting Data.
2024-06-10 08:23:11.062816 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:11.06389 INFO::Removing potential empty rows and columns
2024-06-10 08:23:11.064877 INFO::Found 0 missing values.
2024-06-10 08:23:11.065927 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 08:23:11.074958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:11.075788 INFO::Done
2024-06-10 08:23:11.076248 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:11.083249 INFO::Starting hierarchical adjustment
2024-06-10 08:23:11.084494 INFO::Found 2 batches.
2024-06-10 08:23:11.08503 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:11.085574 INFO::Using default BPPARAM
2024-06-10 08:23:11.088175 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:11.089285 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:11.116766 INFO::Done
2024-06-10 08:23:11.1215 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:11.126188 INFO::ASW Batch was 0.497829960046276 prior to batch effect correction and is now 0.0882226471362079 .
2024-06-10 08:23:11.127426 INFO::ASW Label was 0.554250149992516 prior to batch effect correction and is now 0.867731659794373 .
2024-06-10 08:23:11.128271 INFO::Total function execution time is 0.0689949989318848 s and adjustment time is 0.0324459075927734 s ( 47.03 )
2024-06-10 08:23:11.493909 INFO::Formatting Data.
2024-06-10 08:23:11.498325 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:11.499692 INFO::Removing potential empty rows and columns
2024-06-10 08:23:11.500794 INFO::Found 0 missing values.
2024-06-10 08:23:11.505217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:11.50612 INFO::Done
2024-06-10 08:23:11.506558 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:11.512493 INFO::Starting hierarchical adjustment
2024-06-10 08:23:11.513432 INFO::Found 3 batches.
2024-06-10 08:23:11.516436 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:11.517488 INFO::Using default BPPARAM
2024-06-10 08:23:11.518053 INFO::Processing subtree level 1
2024-06-10 08:23:11.711879 INFO::Adjusting the last 1 batches sequentially
2024-06-10 08:23:11.719433 INFO::Done
2024-06-10 08:23:11.720792 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:11.72471 INFO::ASW Batch was -0.0962005225486997 prior to batch effect correction and is now -0.0962005225486997 .
2024-06-10 08:23:11.726635 INFO::Total function execution time is 0.232794046401978 s and adjustment time is 0.206087827682495 s ( 88.53 )
2024-06-10 08:23:11.727886 INFO::Formatting Data.
2024-06-10 08:23:11.72859 INFO::Typecasting input to dataframe.
2024-06-10 08:23:11.729793 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:11.730717 INFO::Removing potential empty rows and columns
2024-06-10 08:23:11.731805 INFO::Found 0 missing values.
2024-06-10 08:23:11.734619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:11.735361 INFO::Done
2024-06-10 08:23:11.73588 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:11.737911 INFO::Starting hierarchical adjustment
2024-06-10 08:23:11.739395 INFO::Found 3 batches.
2024-06-10 08:23:11.739995 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:11.740566 INFO::Using default BPPARAM
2024-06-10 08:23:11.740978 INFO::Processing subtree level 1
2024-06-10 08:23:11.864018 INFO::Adjusting the last 1 batches sequentially
2024-06-10 08:23:11.870377 INFO::Done
2024-06-10 08:23:11.871508 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:11.881055 INFO::ASW Batch was -0.0962005225486997 prior to batch effect correction and is now -0.0962005225486997 .
2024-06-10 08:23:11.88289 INFO::Total function execution time is 0.154935121536255 s and adjustment time is 0.13110089302063 s ( 84.62 )
2024-06-10 08:23:11.90365 INFO::Formatting Data.
2024-06-10 08:23:11.904573 INFO::Typecasting input to dataframe.
2024-06-10 08:23:11.905362 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:11.910682 INFO::Removing potential empty rows and columns
2024-06-10 08:23:11.912539 INFO::Found 0 missing values.
2024-06-10 08:23:11.918104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:11.918944 INFO::Done
2024-06-10 08:23:11.922689 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:11.925717 INFO::Starting hierarchical adjustment
2024-06-10 08:23:11.931108 INFO::Found 3 batches.
2024-06-10 08:23:11.931874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:11.93249 INFO::Using default BPPARAM
2024-06-10 08:23:11.933044 INFO::Processing subtree level 1
2024-06-10 08:23:12.115156 INFO::Adjusting the last 1 batches sequentially
2024-06-10 08:23:12.125928 INFO::Done
2024-06-10 08:23:12.127585 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:12.136203 INFO::ASW Batch was -0.0395846684237795 prior to batch effect correction and is now -0.0395846684237795 .
2024-06-10 08:23:12.142238 INFO::Total function execution time is 0.238422870635986 s and adjustment time is 0.195230007171631 s ( 81.88 )
2024-06-10 08:23:12.469809 INFO::Formatting Data.
2024-06-10 08:23:12.471046 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:12.476852 INFO::Removing potential empty rows and columns
2024-06-10 08:23:12.47972 INFO::Found 1000 missing values.
2024-06-10 08:23:12.506006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:12.506791 INFO::Done
2024-06-10 08:23:12.507263 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:12.515839 INFO::Starting hierarchical adjustment
2024-06-10 08:23:12.516949 INFO::Found 10 batches.
2024-06-10 08:23:12.517588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:12.52267 INFO::Using default BPPARAM
2024-06-10 08:23:12.523509 INFO::Processing subtree level 1
2024-06-10 08:23:12.76406 INFO::Processing subtree level 2
2024-06-10 08:23:13.020635 INFO::Adjusting the last 1 batches sequentially
2024-06-10 08:23:13.02647 INFO::Done
2024-06-10 08:23:13.02776 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:13.040284 INFO::ASW Batch was 0.502304269403429 prior to batch effect correction and is now 0.502304269403429 .
2024-06-10 08:23:13.041134 INFO::ASW Label was 0.316466071267873 prior to batch effect correction and is now 0.316466071267873 .
2024-06-10 08:23:13.045681 INFO::Total function execution time is 0.575973987579346 s and adjustment time is 0.509691953659058 s ( 88.49 )
2024-06-10 08:23:13.046683 INFO::Formatting Data.
2024-06-10 08:23:13.047202 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:13.050634 INFO::Removing potential empty rows and columns
2024-06-10 08:23:13.053621 INFO::Found 1000 missing values.
2024-06-10 08:23:13.082767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:13.083697 INFO::Done
2024-06-10 08:23:13.087011 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:13.097975 INFO::Starting hierarchical adjustment
2024-06-10 08:23:13.099405 INFO::Found 10 batches.
2024-06-10 08:23:14.684061 INFO::Set up parallel execution backend with 2 workers
2024-06-10 08:23:14.685261 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-10 08:23:17.064184 INFO::Adjusting the last 2 batches sequentially
2024-06-10 08:23:17.066275 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 08:23:17.096501 INFO::Done
2024-06-10 08:23:17.097271 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:17.108615 INFO::ASW Batch was 0.502304269403429 prior to batch effect correction and is now 0.502304269403429 .
2024-06-10 08:23:17.109398 INFO::ASW Label was 0.316466071267873 prior to batch effect correction and is now 0.316466071267873 .
2024-06-10 08:23:17.11018 INFO::Total function execution time is 4.06350302696228 s and adjustment time is 3.99742603302002 s ( 98.37 )
2024-06-10 08:23:17.413905 INFO::Formatting Data.
2024-06-10 08:23:17.415018 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:17.416495 INFO::Removing potential empty rows and columns
2024-06-10 08:23:17.422089 INFO::Found 0 missing values.
2024-06-10 08:23:17.427398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:17.428179 INFO::Done
2024-06-10 08:23:17.42864 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 08:23:17.435284 INFO::Starting hierarchical adjustment
2024-06-10 08:23:17.436273 INFO::Found 3 batches.
2024-06-10 08:23:17.439926 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 08:23:17.441459 INFO::Using default BPPARAM
2024-06-10 08:23:17.442231 INFO::Processing subtree level 1
2024-06-10 08:23:17.686138 INFO::Adjusting the last 1 batches sequentially
2024-06-10 08:23:17.695866 INFO::Done
2024-06-10 08:23:17.697015 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 08:23:17.703692 INFO::ASW Batch was 0.115800518361377 prior to batch effect correction and is now -0.134637918276263 .
2024-06-10 08:23:17.708746 INFO::ASW Label was -0.202061541261381 prior to batch effect correction and is now -0.132918584816496 .
2024-06-10 08:23:17.710228 INFO::Total function execution time is 0.296685934066772 s and adjustment time is 0.259670972824097 s ( 87.52 )
2024-06-10 08:23:17.936256 INFO::Formatting Data.
2024-06-10 08:23:17.937344 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:17.938212 INFO::Removing potential empty rows and columns
2024-06-10 08:23:17.939264 INFO::Found 2 missing values.
2024-06-10 08:23:17.942097 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:17.942814 INFO::Done
2024-06-10 08:23:17.987698 INFO::Found NA in Reference column
2024-06-10 08:23:18.013481 INFO::Require at least two references per batch.
2024-06-10 08:23:18.063915 INFO::Formatting Data.
2024-06-10 08:23:18.064967 INFO::Recognized SummarizedExperiment
2024-06-10 08:23:18.065448 INFO::Typecasting input to dataframe.
2024-06-10 08:23:18.078453 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:18.080051 INFO::Removing potential empty rows and columns
2024-06-10 08:23:18.083743 INFO::Found 0 missing values.
2024-06-10 08:23:18.091321 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:18.09207 INFO::Done
2024-06-10 08:23:18.108323 INFO::Formatting Data.
2024-06-10 08:23:18.109165 INFO::Recognized SummarizedExperiment
2024-06-10 08:23:18.109622 INFO::Typecasting input to dataframe.
2024-06-10 08:23:18.128328 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:18.129796 INFO::Removing potential empty rows and columns
2024-06-10 08:23:18.136214 INFO::Found 0 missing values.
2024-06-10 08:23:18.153792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:18.154565 INFO::Done
2024-06-10 08:23:18.177939 INFO::Formatting Data.
2024-06-10 08:23:18.178801 INFO::Recognized SummarizedExperiment
2024-06-10 08:23:18.179275 INFO::Typecasting input to dataframe.
2024-06-10 08:23:18.197982 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:18.199276 INFO::Removing potential empty rows and columns
2024-06-10 08:23:18.200434 INFO::Found 0 missing values.
2024-06-10 08:23:18.201396 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 08:23:18.205898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:18.206678 INFO::Done
2024-06-10 08:23:18.220663 INFO::Formatting Data.
2024-06-10 08:23:18.221517 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:18.222317 INFO::Removing potential empty rows and columns
2024-06-10 08:23:18.223201 INFO::Found 0 missing values.
2024-06-10 08:23:18.225929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:18.226688 INFO::Done
2024-06-10 08:23:18.240177 INFO::Formatting Data.
2024-06-10 08:23:18.241001 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:18.241742 INFO::Removing potential empty rows and columns
2024-06-10 08:23:18.242588 INFO::Found 0 missing values.
2024-06-10 08:23:18.245054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:18.245682 INFO::Done
2024-06-10 08:23:18.286289 INFO::Formatting Data.
2024-06-10 08:23:18.287379 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:18.288507 INFO::Removing potential empty rows and columns
2024-06-10 08:23:18.289834 INFO::Found 1 missing values.
2024-06-10 08:23:18.293391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:18.294182 INFO::Done
2024-06-10 08:23:18.320866 INFO::Formatting Data.
2024-06-10 08:23:18.321935 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:18.322948 INFO::Removing potential empty rows and columns
2024-06-10 08:23:18.324041 INFO::Found 2 missing values.
2024-06-10 08:23:18.325203 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 08:23:18.327856 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:18.328662 INFO::Done
2024-06-10 08:23:18.342666 INFO::Formatting Data.
2024-06-10 08:23:18.34375 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:18.345036 INFO::Removing potential empty rows and columns
2024-06-10 08:23:18.346598 INFO::Found 2 missing values.
2024-06-10 08:23:18.349174 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:18.350321 INFO::Done
2024-06-10 08:23:18.366552 INFO::Formatting Data.
2024-06-10 08:23:18.36761 INFO::Typecasting input to dataframe.
2024-06-10 08:23:18.36843 INFO::Replacing NaNs with NAs.
2024-06-10 08:23:18.369465 INFO::Removing potential empty rows and columns
2024-06-10 08:23:18.370628 INFO::Found 0 missing values.
2024-06-10 08:23:18.373958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 08:23:18.374722 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
23.180 3.526 38.806
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 32.301 | 1.306 | 34.022 | |
| compute_asw | 0.028 | 0.001 | 0.043 | |
| count_existing | 0.016 | 0.001 | 0.018 | |
| generate_data_covariables | 0.014 | 0.001 | 0.024 | |
| generate_dataset | 0.013 | 0.001 | 0.018 | |