Yannis Schumann
| Snapshot Date: 2024-05-01 14:05:06 -0400 (Wed, 01 May 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-03 11:38:09 -0400 (Fri, 03 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 154/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.0 |
| Command: /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_1.1.0.tar.gz |
| StartedAt: 2024-05-02 00:39:14 -0400 (Thu, 02 May 2024) |
| EndedAt: 2024-05-02 00:41:49 -0400 (Thu, 02 May 2024) |
| EllapsedTime: 155.2 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-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 Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 45.733 2.638 39.506
* 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-x86_64/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 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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")
2024-05-02 00:41:11.222569 INFO::Formatting Data.
2024-05-02 00:41:11.231139 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:11.267426 INFO::Removing potential empty rows and columns
2024-05-02 00:41:12.09156 INFO::Found 0 missing values.
2024-05-02 00:41:12.103625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:12.105265 INFO::Done
2024-05-02 00:41:12.107307 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:12.140498 INFO::Starting hierarchical adjustment
2024-05-02 00:41:12.142686 INFO::Found 3 batches.
2024-05-02 00:41:12.14409 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:12.146988 INFO::Using default BPPARAM
2024-05-02 00:41:12.148408 INFO::Processing subtree level 1
2024-05-02 00:41:12.438717 INFO::Adjusting the last 1 batches sequentially
2024-05-02 00:41:12.442996 INFO::Done
2024-05-02 00:41:12.444574 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:12.45073 INFO::ASW Batch was -0.0584012587629114 prior to batch effect correction and is now -0.0584012587629114 .
2024-05-02 00:41:12.453399 INFO::Total function execution time is 1.23222708702087 s and adjustment time is 0.300955057144165 s ( 24.42 )
2024-05-02 00:41:12.498082 INFO::Formatting Data.
2024-05-02 00:41:12.499861 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:12.502358 INFO::Removing potential empty rows and columns
2024-05-02 00:41:12.507122 INFO::Found 0 missing values.
2024-05-02 00:41:12.509865 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-02 00:41:12.541844 INFO::Formatting Data.
2024-05-02 00:41:12.543606 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:12.545963 INFO::Removing potential empty rows and columns
2024-05-02 00:41:12.548986 INFO::Found 0 missing values.
2024-05-02 00:41:12.551561 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-02 00:41:12.606416 INFO::Formatting Data.
2024-05-02 00:41:12.609351 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:12.611776 INFO::Removing potential empty rows and columns
2024-05-02 00:41:12.614396 INFO::Found 0 missing values.
2024-05-02 00:41:12.616667 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-02 00:41:12.631231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:12.632671 INFO::Done
2024-05-02 00:41:12.6339 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:12.639662 INFO::Starting hierarchical adjustment
2024-05-02 00:41:12.641579 INFO::Found 2 batches.
2024-05-02 00:41:12.642981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:12.644657 INFO::Using default BPPARAM
2024-05-02 00:41:12.64604 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:12.648413 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:12.715836 INFO::Done
2024-05-02 00:41:12.71741 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:12.723998 INFO::ASW Batch was -0.0221013694120634 prior to batch effect correction and is now -0.117355403461419 .
2024-05-02 00:41:12.726124 INFO::Total function execution time is 0.119839906692505 s and adjustment time is 0.0746119022369385 s ( 62.26 )
2024-05-02 00:41:12.73346 INFO::Formatting Data.
2024-05-02 00:41:12.735153 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:12.760241 INFO::Formatting Data.
2024-05-02 00:41:12.761854 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:12.763946 INFO::Removing potential empty rows and columns
2024-05-02 00:41:12.766574 INFO::Found 0 missing values.
2024-05-02 00:41:12.776847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:12.778332 INFO::Done
2024-05-02 00:41:12.779646 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:12.784631 INFO::Starting hierarchical adjustment
2024-05-02 00:41:12.788232 INFO::Found 2 batches.
2024-05-02 00:41:12.789557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:12.791116 INFO::Using default BPPARAM
2024-05-02 00:41:12.792446 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:12.79512 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:12.845326 INFO::Done
2024-05-02 00:41:12.846769 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:12.851956 INFO::ASW Batch was -0.060016914435948 prior to batch effect correction and is now -0.110547550988017 .
2024-05-02 00:41:12.85628 INFO::Total function execution time is 0.096066951751709 s and adjustment time is 0.0574970245361328 s ( 59.85 )
2024-05-02 00:41:12.859048 INFO::Formatting Data.
2024-05-02 00:41:12.860618 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:12.8628 INFO::Removing potential empty rows and columns
2024-05-02 00:41:12.867437 INFO::Found 0 missing values.
2024-05-02 00:41:12.875872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:12.877317 INFO::Done
2024-05-02 00:41:12.879729 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:12.884967 INFO::Starting hierarchical adjustment
2024-05-02 00:41:12.886869 INFO::Found 2 batches.
2024-05-02 00:41:12.888196 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:12.892243 INFO::Using default BPPARAM
2024-05-02 00:41:12.893709 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:12.895955 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:12.940736 INFO::Done
2024-05-02 00:41:12.942238 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:12.948008 INFO::ASW Batch was -0.060016914435948 prior to batch effect correction and is now -0.110547550988017 .
2024-05-02 00:41:12.950054 INFO::Total function execution time is 0.0910160541534424 s and adjustment time is 0.0542261600494385 s ( 59.58 )
2024-05-02 00:41:19.064449 INFO::Formatting Data.
2024-05-02 00:41:19.06592 INFO::Recognized SummarizedExperiment
2024-05-02 00:41:19.06701 INFO::Typecasting input to dataframe.
2024-05-02 00:41:20.193567 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:20.195747 INFO::Removing potential empty rows and columns
2024-05-02 00:41:20.206289 INFO::Found 0 missing values.
2024-05-02 00:41:20.228421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:20.229648 INFO::Done
2024-05-02 00:41:20.230699 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:20.239513 INFO::Starting hierarchical adjustment
2024-05-02 00:41:20.241644 INFO::Found 2 batches.
2024-05-02 00:41:20.242774 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:20.244858 INFO::Using default BPPARAM
2024-05-02 00:41:20.246081 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:20.248212 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:20.419957 INFO::Done
2024-05-02 00:41:20.421266 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:20.430176 INFO::ASW Batch was 0.0341895671875179 prior to batch effect correction and is now -0.0924565873842182 .
2024-05-02 00:41:20.431957 INFO::Total function execution time is 1.37083792686462 s and adjustment time is 0.178647994995117 s ( 13.03 )
2024-05-02 00:41:20.482823 INFO::Formatting Data.
2024-05-02 00:41:20.484131 INFO::Recognized SummarizedExperiment
2024-05-02 00:41:20.48509 INFO::Typecasting input to dataframe.
2024-05-02 00:41:20.511777 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:20.514761 INFO::Removing potential empty rows and columns
2024-05-02 00:41:20.525761 INFO::Found 0 missing values.
2024-05-02 00:41:20.545743 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:20.549601 INFO::Done
2024-05-02 00:41:20.550865 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:20.558773 INFO::Starting hierarchical adjustment
2024-05-02 00:41:20.561437 INFO::Found 2 batches.
2024-05-02 00:41:20.564161 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:20.56566 INFO::Using default BPPARAM
2024-05-02 00:41:20.566835 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:20.568991 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:20.644981 INFO::Done
2024-05-02 00:41:20.646386 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:20.658205 INFO::ASW Batch was -0.00269696781335294 prior to batch effect correction and is now -0.00269696781335294 .
2024-05-02 00:41:20.660069 INFO::Total function execution time is 0.177156925201416 s and adjustment time is 0.0839219093322754 s ( 47.37 )
2024-05-02 00:41:20.710868 INFO::Formatting Data.
2024-05-02 00:41:20.712536 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:20.714427 INFO::Removing potential empty rows and columns
2024-05-02 00:41:20.719561 INFO::Found 0 missing values.
2024-05-02 00:41:20.726075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:20.727813 INFO::Done
2024-05-02 00:41:20.729085 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:20.734561 INFO::Starting hierarchical adjustment
2024-05-02 00:41:20.736188 INFO::Found 3 batches.
2024-05-02 00:41:20.73784 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:20.740821 INFO::Using default BPPARAM
2024-05-02 00:41:20.742243 INFO::Processing subtree level 1
2024-05-02 00:41:21.203672 INFO::Adjusting the last 1 batches sequentially
2024-05-02 00:41:21.212444 INFO::Done
2024-05-02 00:41:21.214211 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:21.226438 INFO::ASW Batch was -0.00183925360099998 prior to batch effect correction and is now -0.146204410582747 .
2024-05-02 00:41:21.231231 INFO::Total function execution time is 0.518640995025635 s and adjustment time is 0.476543188095093 s ( 91.88 )
2024-05-02 00:41:21.270969 INFO::Skipping initial DF formatting
2024-05-02 00:41:21.272494 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:21.282174 INFO::Starting hierarchical adjustment
2024-05-02 00:41:21.284122 INFO::Found 5 batches.
2024-05-02 00:41:21.285512 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:21.287175 INFO::Using default BPPARAM
2024-05-02 00:41:21.288592 INFO::Processing subtree level 1
2024-05-02 00:41:21.654103 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:21.664757 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:21.73837 INFO::Done
2024-05-02 00:41:21.739896 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:21.751663 INFO::ASW Batch was 0.501098168555545 prior to batch effect correction and is now 0.501098168555545 .
2024-05-02 00:41:21.754022 INFO::ASW Label was 0.386380433133024 prior to batch effect correction and is now 0.386380433133024 .
2024-05-02 00:41:21.756948 INFO::Total function execution time is 0.486009120941162 s and adjustment time is 0.454597949981689 s ( 93.54 )
2024-05-02 00:41:21.811244 INFO::Formatting Data.
2024-05-02 00:41:21.812994 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:21.815216 INFO::Removing potential empty rows and columns
2024-05-02 00:41:21.817777 INFO::Found 0 missing values.
2024-05-02 00:41:21.830471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:21.831918 INFO::Done
2024-05-02 00:41:21.833146 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:21.842618 INFO::Starting hierarchical adjustment
2024-05-02 00:41:21.846035 INFO::Found 5 batches.
2024-05-02 00:41:21.848074 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:21.850574 INFO::Using default BPPARAM
2024-05-02 00:41:21.852149 INFO::Processing subtree level 1
2024-05-02 00:41:22.134165 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:22.144978 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:22.198888 INFO::Done
2024-05-02 00:41:22.200348 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:22.208007 INFO::ASW Batch was 0.432105562275358 prior to batch effect correction and is now -0.102731614600839 .
2024-05-02 00:41:22.209965 INFO::ASW Label was 0.311781934431278 prior to batch effect correction and is now 0.874661123182458 .
2024-05-02 00:41:22.212882 INFO::Total function execution time is 0.401721000671387 s and adjustment time is 0.353308916091919 s ( 87.95 )
2024-05-02 00:41:22.214954 INFO::Formatting Data.
2024-05-02 00:41:22.216876 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:22.219411 INFO::Removing potential empty rows and columns
2024-05-02 00:41:22.222016 INFO::Found 0 missing values.
2024-05-02 00:41:22.233673 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:22.235052 INFO::Done
2024-05-02 00:41:22.237471 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:22.244645 INFO::Starting hierarchical adjustment
2024-05-02 00:41:22.246532 INFO::Found 5 batches.
2024-05-02 00:41:22.247864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:22.250751 INFO::Using default BPPARAM
2024-05-02 00:41:22.252143 INFO::Processing subtree level 1
2024-05-02 00:41:22.516844 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:22.526866 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:22.579124 INFO::Done
2024-05-02 00:41:22.580544 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:22.588822 INFO::ASW Batch was 0.432105562275358 prior to batch effect correction and is now -0.102731614600839 .
2024-05-02 00:41:22.590355 INFO::ASW Label was 0.311781934431278 prior to batch effect correction and is now 0.874661123182458 .
2024-05-02 00:41:22.593546 INFO::Total function execution time is 0.378496885299683 s and adjustment time is 0.332941055297852 s ( 87.96 )
2024-05-02 00:41:22.637864 INFO::Formatting Data.
2024-05-02 00:41:22.639565 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:22.642981 INFO::Removing potential empty rows and columns
2024-05-02 00:41:22.645671 INFO::Found 0 missing values.
2024-05-02 00:41:22.658028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:22.659479 INFO::Done
2024-05-02 00:41:22.660804 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:22.667847 INFO::Starting hierarchical adjustment
2024-05-02 00:41:22.670088 INFO::Found 5 batches.
2024-05-02 00:41:22.671388 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:22.67291 INFO::Using default BPPARAM
2024-05-02 00:41:22.674293 INFO::Processing subtree level 1
2024-05-02 00:41:22.941772 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:22.950675 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:23.003581 INFO::Done
2024-05-02 00:41:23.005174 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:23.01979 INFO::ASW Batch was 0.680311574412785 prior to batch effect correction and is now -0.0677701140658718 .
2024-05-02 00:41:23.021446 INFO::ASW Label was 0.100803875128136 prior to batch effect correction and is now 0.78864782479239 .
2024-05-02 00:41:23.023821 INFO::Total function execution time is 0.385958909988403 s and adjustment time is 0.333978891372681 s ( 86.53 )
2024-05-02 00:41:23.026654 INFO::Formatting Data.
2024-05-02 00:41:23.028396 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:23.030673 INFO::Removing potential empty rows and columns
2024-05-02 00:41:23.033222 INFO::Found 0 missing values.
2024-05-02 00:41:23.044429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:23.045867 INFO::Done
2024-05-02 00:41:23.047098 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:23.053921 INFO::Starting hierarchical adjustment
2024-05-02 00:41:23.055822 INFO::Found 5 batches.
2024-05-02 00:41:23.057041 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:23.058543 INFO::Using default BPPARAM
2024-05-02 00:41:23.059886 INFO::Processing subtree level 1
2024-05-02 00:41:23.316133 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:23.330435 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:23.390176 INFO::Done
2024-05-02 00:41:23.391556 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:23.401961 INFO::ASW Batch was 0.680311574412785 prior to batch effect correction and is now -0.0677701140658718 .
2024-05-02 00:41:23.403563 INFO::ASW Label was 0.100803875128136 prior to batch effect correction and is now 0.78864782479239 .
2024-05-02 00:41:23.40606 INFO::Total function execution time is 0.379830837249756 s and adjustment time is 0.334756135940552 s ( 88.13 )
2024-05-02 00:41:23.442134 INFO::Formatting Data.
2024-05-02 00:41:23.443882 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:23.44608 INFO::Removing potential empty rows and columns
2024-05-02 00:41:23.448766 INFO::Found 0 missing values.
2024-05-02 00:41:23.459012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:23.460513 INFO::Done
2024-05-02 00:41:23.46187 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:23.47021 INFO::Starting hierarchical adjustment
2024-05-02 00:41:23.472172 INFO::Found 2 batches.
2024-05-02 00:41:23.477206 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:23.479047 INFO::Using default BPPARAM
2024-05-02 00:41:23.481753 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:23.484473 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:23.536037 INFO::Done
2024-05-02 00:41:23.537555 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:23.544627 INFO::ASW Batch was 0.548918566315095 prior to batch effect correction and is now -0.0366729191835491 .
2024-05-02 00:41:23.546112 INFO::ASW Label was 0.525003544843081 prior to batch effect correction and is now 0.925168364968188 .
2024-05-02 00:41:23.548174 INFO::Total function execution time is 0.106149911880493 s and adjustment time is 0.0642688274383545 s ( 60.55 )
2024-05-02 00:41:23.550227 INFO::Formatting Data.
2024-05-02 00:41:23.551708 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:23.553694 INFO::Removing potential empty rows and columns
2024-05-02 00:41:23.556252 INFO::Found 0 missing values.
2024-05-02 00:41:23.56507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:23.566683 INFO::Done
2024-05-02 00:41:23.568071 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:23.579508 INFO::Starting hierarchical adjustment
2024-05-02 00:41:23.582238 INFO::Found 2 batches.
2024-05-02 00:41:23.583794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:23.585559 INFO::Using default BPPARAM
2024-05-02 00:41:23.589681 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:23.592598 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:23.639885 INFO::Done
2024-05-02 00:41:23.64153 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:23.649999 INFO::ASW Batch was 0.548918566315095 prior to batch effect correction and is now -0.0366729191835491 .
2024-05-02 00:41:23.651595 INFO::ASW Label was 0.525003544843081 prior to batch effect correction and is now 0.925168364968188 .
2024-05-02 00:41:23.653635 INFO::Total function execution time is 0.103425025939941 s and adjustment time is 0.0580852031707764 s ( 56.16 )
2024-05-02 00:41:23.691999 INFO::Formatting Data.
2024-05-02 00:41:23.693788 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:23.695938 INFO::Removing potential empty rows and columns
2024-05-02 00:41:23.699984 INFO::Found 0 missing values.
2024-05-02 00:41:23.70574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:23.707207 INFO::Done
2024-05-02 00:41:23.711972 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:23.717048 INFO::Starting hierarchical adjustment
2024-05-02 00:41:23.718846 INFO::Found 2 batches.
2024-05-02 00:41:23.720152 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:23.72275 INFO::Using default BPPARAM
2024-05-02 00:41:23.724099 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:23.72627 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:23.819479 INFO::Done
2024-05-02 00:41:23.821024 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:23.826606 INFO::ASW Batch was -0.0755015378959997 prior to batch effect correction and is now -0.155069738966349 .
2024-05-02 00:41:23.828633 INFO::Total function execution time is 0.136729001998901 s and adjustment time is 0.100890874862671 s ( 73.79 )
2024-05-02 00:41:23.867369 INFO::Formatting Data.
2024-05-02 00:41:23.872089 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:23.874332 INFO::Removing potential empty rows and columns
2024-05-02 00:41:23.878011 INFO::Found 0 missing values.
2024-05-02 00:41:23.88091 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-02 00:41:23.899762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:23.90122 INFO::Done
2024-05-02 00:41:23.902517 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:23.911796 INFO::Starting hierarchical adjustment
2024-05-02 00:41:23.913699 INFO::Found 2 batches.
2024-05-02 00:41:23.915573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:23.917093 INFO::Using default BPPARAM
2024-05-02 00:41:23.918271 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:23.920447 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:23.976099 INFO::Done
2024-05-02 00:41:23.977793 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:23.985265 INFO::ASW Batch was 0.438391263622737 prior to batch effect correction and is now 0.000134738442059945 .
2024-05-02 00:41:23.988064 INFO::ASW Label was 0.573289196337161 prior to batch effect correction and is now 0.917597923677553 .
2024-05-02 00:41:23.9899 INFO::Total function execution time is 0.122647047042847 s and adjustment time is 0.0617618560791016 s ( 50.36 )
2024-05-02 00:41:23.991615 INFO::Formatting Data.
2024-05-02 00:41:23.99309 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:23.995396 INFO::Removing potential empty rows and columns
2024-05-02 00:41:23.999926 INFO::Found 0 missing values.
2024-05-02 00:41:24.002311 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-02 00:41:24.017601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:24.019063 INFO::Done
2024-05-02 00:41:24.020353 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:24.029575 INFO::Starting hierarchical adjustment
2024-05-02 00:41:24.031413 INFO::Found 2 batches.
2024-05-02 00:41:24.03299 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:24.036746 INFO::Using default BPPARAM
2024-05-02 00:41:24.038309 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:24.040878 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:24.088844 INFO::Done
2024-05-02 00:41:24.090209 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:24.100488 INFO::ASW Batch was 0.438391263622737 prior to batch effect correction and is now 0.000134738442059945 .
2024-05-02 00:41:24.102031 INFO::ASW Label was 0.573289196337161 prior to batch effect correction and is now 0.917597923677553 .
2024-05-02 00:41:24.10492 INFO::Total function execution time is 0.113274097442627 s and adjustment time is 0.0578041076660156 s ( 51.03 )
2024-05-02 00:41:24.815445 INFO::Formatting Data.
2024-05-02 00:41:24.817864 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:24.819989 INFO::Removing potential empty rows and columns
2024-05-02 00:41:24.823214 INFO::Found 0 missing values.
2024-05-02 00:41:24.83129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:24.832603 INFO::Done
2024-05-02 00:41:24.83495 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:24.841474 INFO::Starting hierarchical adjustment
2024-05-02 00:41:24.84369 INFO::Found 3 batches.
2024-05-02 00:41:24.845044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:24.847987 INFO::Using default BPPARAM
2024-05-02 00:41:24.849489 INFO::Processing subtree level 1
2024-05-02 00:41:25.098168 INFO::Adjusting the last 1 batches sequentially
2024-05-02 00:41:25.107909 INFO::Done
2024-05-02 00:41:25.10948 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:25.121411 INFO::ASW Batch was -0.0308643849959121 prior to batch effect correction and is now -0.0308643849959121 .
2024-05-02 00:41:25.127311 INFO::Total function execution time is 0.310914993286133 s and adjustment time is 0.264612913131714 s ( 85.11 )
2024-05-02 00:41:25.130121 INFO::Formatting Data.
2024-05-02 00:41:25.131735 INFO::Typecasting input to dataframe.
2024-05-02 00:41:25.133598 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:25.138777 INFO::Removing potential empty rows and columns
2024-05-02 00:41:25.142278 INFO::Found 0 missing values.
2024-05-02 00:41:25.15411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:25.155583 INFO::Done
2024-05-02 00:41:25.156878 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:25.161708 INFO::Starting hierarchical adjustment
2024-05-02 00:41:25.163676 INFO::Found 3 batches.
2024-05-02 00:41:25.165017 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:25.166613 INFO::Using default BPPARAM
2024-05-02 00:41:25.167939 INFO::Processing subtree level 1
2024-05-02 00:41:25.410217 INFO::Adjusting the last 1 batches sequentially
2024-05-02 00:41:25.41903 INFO::Done
2024-05-02 00:41:25.420944 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:25.431856 INFO::ASW Batch was -0.0308643849959121 prior to batch effect correction and is now -0.0308643849959121 .
2024-05-02 00:41:25.437453 INFO::Total function execution time is 0.306827068328857 s and adjustment time is 0.255730867385864 s ( 83.35 )
2024-05-02 00:41:25.476562 INFO::Formatting Data.
2024-05-02 00:41:25.478185 INFO::Typecasting input to dataframe.
2024-05-02 00:41:25.480108 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:25.48263 INFO::Removing potential empty rows and columns
2024-05-02 00:41:25.485347 INFO::Found 0 missing values.
2024-05-02 00:41:25.493338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:25.495122 INFO::Done
2024-05-02 00:41:25.49815 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:25.504474 INFO::Starting hierarchical adjustment
2024-05-02 00:41:25.506777 INFO::Found 3 batches.
2024-05-02 00:41:25.511052 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:25.516084 INFO::Using default BPPARAM
2024-05-02 00:41:25.517584 INFO::Processing subtree level 1
2024-05-02 00:41:25.751576 INFO::Adjusting the last 1 batches sequentially
2024-05-02 00:41:25.758616 INFO::Done
2024-05-02 00:41:25.761053 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:25.77288 INFO::ASW Batch was -0.0308718773400295 prior to batch effect correction and is now -0.0308718773400295 .
2024-05-02 00:41:25.777601 INFO::Total function execution time is 0.300003051757812 s and adjustment time is 0.252178907394409 s ( 84.06 )
2024-05-02 00:41:26.185969 INFO::Formatting Data.
2024-05-02 00:41:26.188477 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:26.191639 INFO::Removing potential empty rows and columns
2024-05-02 00:41:26.201274 INFO::Found 1000 missing values.
2024-05-02 00:41:26.283715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:26.285327 INFO::Done
2024-05-02 00:41:26.287423 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:26.300146 INFO::Starting hierarchical adjustment
2024-05-02 00:41:26.302644 INFO::Found 10 batches.
2024-05-02 00:41:26.303956 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:26.305343 INFO::Using default BPPARAM
2024-05-02 00:41:26.307568 INFO::Processing subtree level 1
2024-05-02 00:41:26.647365 INFO::Processing subtree level 2
2024-05-02 00:41:27.088744 INFO::Adjusting the last 1 batches sequentially
2024-05-02 00:41:27.100159 INFO::Done
2024-05-02 00:41:27.10161 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:27.120718 INFO::ASW Batch was 0.507064589589974 prior to batch effect correction and is now 0.507064589589974 .
2024-05-02 00:41:27.122118 INFO::ASW Label was 0.322633464513659 prior to batch effect correction and is now 0.322633464513659 .
2024-05-02 00:41:27.128905 INFO::Total function execution time is 0.942571878433228 s and adjustment time is 0.797899007797241 s ( 84.65 )
2024-05-02 00:41:27.132668 INFO::Formatting Data.
2024-05-02 00:41:27.134208 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:27.136857 INFO::Removing potential empty rows and columns
2024-05-02 00:41:27.146038 INFO::Found 1000 missing values.
2024-05-02 00:41:27.20744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:27.208726 INFO::Done
2024-05-02 00:41:27.209893 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:27.221473 INFO::Starting hierarchical adjustment
2024-05-02 00:41:27.223898 INFO::Found 10 batches.
2024-05-02 00:41:28.693816 INFO::Set up parallel execution backend with 2 workers
2024-05-02 00:41:28.695141 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-02 00:41:30.662214 INFO::Adjusting the last 2 batches sequentially
2024-05-02 00:41:30.664625 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-02 00:41:30.721233 INFO::Done
2024-05-02 00:41:30.72258 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:30.73653 INFO::ASW Batch was 0.507064589589974 prior to batch effect correction and is now 0.507064589589974 .
2024-05-02 00:41:30.739077 INFO::ASW Label was 0.322633464513659 prior to batch effect correction and is now 0.322633464513659 .
2024-05-02 00:41:30.74086 INFO::Total function execution time is 3.6083390712738 s and adjustment time is 3.49771404266357 s ( 96.93 )
2024-05-02 00:41:31.179161 INFO::Formatting Data.
2024-05-02 00:41:31.180956 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:31.183084 INFO::Removing potential empty rows and columns
2024-05-02 00:41:31.185865 INFO::Found 0 missing values.
2024-05-02 00:41:31.196896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:31.198251 INFO::Done
2024-05-02 00:41:31.199448 INFO::Acquiring quality metrics before batch effect correction.
2024-05-02 00:41:31.207476 INFO::Starting hierarchical adjustment
2024-05-02 00:41:31.209346 INFO::Found 3 batches.
2024-05-02 00:41:31.210709 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-02 00:41:31.21364 INFO::Using default BPPARAM
2024-05-02 00:41:31.215143 INFO::Processing subtree level 1
2024-05-02 00:41:31.530672 INFO::Adjusting the last 1 batches sequentially
2024-05-02 00:41:31.542565 INFO::Done
2024-05-02 00:41:31.544941 INFO::Acquiring quality metrics after batch effect correction.
2024-05-02 00:41:31.562998 INFO::ASW Batch was 0.143417724768404 prior to batch effect correction and is now -0.153345832169083 .
2024-05-02 00:41:31.564613 INFO::ASW Label was -0.20441546113062 prior to batch effect correction and is now 0.0916811155505375 .
2024-05-02 00:41:31.57171 INFO::Total function execution time is 0.391504049301147 s and adjustment time is 0.333574056625366 s ( 85.2 )
2024-05-02 00:41:31.946324 INFO::Formatting Data.
2024-05-02 00:41:31.948201 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:31.952708 INFO::Removing potential empty rows and columns
2024-05-02 00:41:31.955743 INFO::Found 2 missing values.
2024-05-02 00:41:31.966457 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:31.967885 INFO::Done
2024-05-02 00:41:32.092931 INFO::Found NA in Reference column
2024-05-02 00:41:32.131982 INFO::Require at least two references per batch.
2024-05-02 00:41:32.20115 INFO::Formatting Data.
2024-05-02 00:41:32.202695 INFO::Recognized SummarizedExperiment
2024-05-02 00:41:32.203938 INFO::Typecasting input to dataframe.
2024-05-02 00:41:32.234982 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:32.238031 INFO::Removing potential empty rows and columns
2024-05-02 00:41:32.252139 INFO::Found 0 missing values.
2024-05-02 00:41:32.280501 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:32.282363 INFO::Done
2024-05-02 00:41:32.329596 INFO::Formatting Data.
2024-05-02 00:41:32.331565 INFO::Recognized SummarizedExperiment
2024-05-02 00:41:32.333443 INFO::Typecasting input to dataframe.
2024-05-02 00:41:32.390352 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:32.393178 INFO::Removing potential empty rows and columns
2024-05-02 00:41:32.407335 INFO::Found 0 missing values.
2024-05-02 00:41:32.455223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:32.456647 INFO::Done
2024-05-02 00:41:32.49969 INFO::Formatting Data.
2024-05-02 00:41:32.501616 INFO::Recognized SummarizedExperiment
2024-05-02 00:41:32.502968 INFO::Typecasting input to dataframe.
2024-05-02 00:41:32.559507 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:32.56172 INFO::Removing potential empty rows and columns
2024-05-02 00:41:32.565625 INFO::Found 0 missing values.
2024-05-02 00:41:32.569073 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-02 00:41:32.582934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:32.585597 INFO::Done
2024-05-02 00:41:32.620769 INFO::Formatting Data.
2024-05-02 00:41:32.622535 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:32.624747 INFO::Removing potential empty rows and columns
2024-05-02 00:41:32.629727 INFO::Found 0 missing values.
2024-05-02 00:41:32.639116 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:32.640662 INFO::Done
2024-05-02 00:41:32.674369 INFO::Formatting Data.
2024-05-02 00:41:32.676089 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:32.678168 INFO::Removing potential empty rows and columns
2024-05-02 00:41:32.681177 INFO::Found 0 missing values.
2024-05-02 00:41:32.690649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:32.692102 INFO::Done
2024-05-02 00:41:32.78592 INFO::Formatting Data.
2024-05-02 00:41:32.787684 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:32.790279 INFO::Removing potential empty rows and columns
2024-05-02 00:41:32.793406 INFO::Found 1 missing values.
2024-05-02 00:41:32.801791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:32.803652 INFO::Done
2024-05-02 00:41:32.861653 INFO::Formatting Data.
2024-05-02 00:41:32.863438 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:32.865954 INFO::Removing potential empty rows and columns
2024-05-02 00:41:32.869015 INFO::Found 2 missing values.
2024-05-02 00:41:32.871485 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-05-02 00:41:32.878208 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:32.879596 INFO::Done
2024-05-02 00:41:32.911925 INFO::Formatting Data.
2024-05-02 00:41:32.913682 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:32.915841 INFO::Removing potential empty rows and columns
2024-05-02 00:41:32.9181 INFO::Found 2 missing values.
2024-05-02 00:41:32.924599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:32.92654 INFO::Done
2024-05-02 00:41:32.960723 INFO::Formatting Data.
2024-05-02 00:41:32.962452 INFO::Typecasting input to dataframe.
2024-05-02 00:41:32.966005 INFO::Replacing NaNs with NAs.
2024-05-02 00:41:32.969078 INFO::Removing potential empty rows and columns
2024-05-02 00:41:32.971928 INFO::Found 0 missing values.
2024-05-02 00:41:32.981752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-02 00:41:32.983859 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.649 6.144 47.775
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 45.733 | 2.638 | 39.506 | |
| compute_asw | 0.057 | 0.002 | 0.064 | |
| count_existing | 0.028 | 0.002 | 0.034 | |
| generate_data_covariables | 0.026 | 0.002 | 0.034 | |
| generate_dataset | 0.024 | 0.001 | 0.029 | |