Yannis Schumann
| Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 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 2024-05-31 17:02:50 -0400 (Fri, 31 May 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" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 | | ||||||||
| 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-05-31 01:32:13 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 01:33:37 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 84.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 22.714 1.083 16.377
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-05-31 01:33:02.521145 INFO::Formatting Data.
2024-05-31 01:33:02.522517 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:02.532843 INFO::Removing potential empty rows and columns
2024-05-31 01:33:02.796354 INFO::Found 0 missing values.
2024-05-31 01:33:02.799508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:02.800122 INFO::Done
2024-05-31 01:33:02.80065 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:02.812148 INFO::Starting hierarchical adjustment
2024-05-31 01:33:02.813008 INFO::Found 3 batches.
2024-05-31 01:33:02.813548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:02.81466 INFO::Using default BPPARAM
2024-05-31 01:33:02.815234 INFO::Processing subtree level 1
2024-05-31 01:33:02.908696 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:33:02.910597 INFO::Done
2024-05-31 01:33:02.911263 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:02.913764 INFO::ASW Batch was -0.0654298279540615 prior to batch effect correction and is now -0.0654298279540615 .
2024-05-31 01:33:02.914824 INFO::Total function execution time is 0.394495725631714 s and adjustment time is 0.0977485179901123 s ( 24.78 )
2024-05-31 01:33:02.928569 INFO::Formatting Data.
2024-05-31 01:33:02.929354 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:02.93032 INFO::Removing potential empty rows and columns
2024-05-31 01:33:02.931422 INFO::Found 0 missing values.
2024-05-31 01:33:02.932399 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.
2024-05-31 01:33:02.943405 INFO::Formatting Data.
2024-05-31 01:33:02.944173 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:02.945123 INFO::Removing potential empty rows and columns
2024-05-31 01:33:02.946229 INFO::Found 0 missing values.
2024-05-31 01:33:02.947171 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.
2024-05-31 01:33:02.962827 INFO::Formatting Data.
2024-05-31 01:33:02.963587 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:02.964493 INFO::Removing potential empty rows and columns
2024-05-31 01:33:02.965491 INFO::Found 0 missing values.
2024-05-31 01:33:02.966363 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.
2024-05-31 01:33:02.970585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:02.9711 INFO::Done
2024-05-31 01:33:02.971595 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:02.973547 INFO::Starting hierarchical adjustment
2024-05-31 01:33:02.974204 INFO::Found 2 batches.
2024-05-31 01:33:02.974699 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:02.9753 INFO::Using default BPPARAM
2024-05-31 01:33:02.975795 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:02.97668 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:02.997669 INFO::Done
2024-05-31 01:33:02.998312 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:03.000255 INFO::ASW Batch was -0.0569023971469615 prior to batch effect correction and is now -0.120215596907066 .
2024-05-31 01:33:03.001022 INFO::Total function execution time is 0.0382962226867676 s and adjustment time is 0.0235776901245117 s ( 61.57 )
2024-05-31 01:33:03.003591 INFO::Formatting Data.
2024-05-31 01:33:03.004182 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:03.01233 INFO::Formatting Data.
2024-05-31 01:33:03.012984 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:03.013811 INFO::Removing potential empty rows and columns
2024-05-31 01:33:03.014776 INFO::Found 0 missing values.
2024-05-31 01:33:03.017512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:03.018019 INFO::Done
2024-05-31 01:33:03.018512 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:03.02041 INFO::Starting hierarchical adjustment
2024-05-31 01:33:03.02107 INFO::Found 2 batches.
2024-05-31 01:33:03.021563 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:03.02212 INFO::Using default BPPARAM
2024-05-31 01:33:03.022631 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:03.023482 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:03.037791 INFO::Done
2024-05-31 01:33:03.038475 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:03.040452 INFO::ASW Batch was -0.0581941952809411 prior to batch effect correction and is now -0.129081705034283 .
2024-05-31 01:33:03.041239 INFO::Total function execution time is 0.0289325714111328 s and adjustment time is 0.0168371200561523 s ( 58.19 )
2024-05-31 01:33:03.042331 INFO::Formatting Data.
2024-05-31 01:33:03.042921 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:03.043769 INFO::Removing potential empty rows and columns
2024-05-31 01:33:03.04479 INFO::Found 0 missing values.
2024-05-31 01:33:03.047496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:03.047996 INFO::Done
2024-05-31 01:33:03.048493 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:03.05041 INFO::Starting hierarchical adjustment
2024-05-31 01:33:03.051062 INFO::Found 2 batches.
2024-05-31 01:33:03.051553 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:03.052136 INFO::Using default BPPARAM
2024-05-31 01:33:03.05264 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:03.053492 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:03.067641 INFO::Done
2024-05-31 01:33:03.06831 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:03.070253 INFO::ASW Batch was -0.0581941952809411 prior to batch effect correction and is now -0.129081705034283 .
2024-05-31 01:33:03.071 INFO::Total function execution time is 0.0287082195281982 s and adjustment time is 0.0167112350463867 s ( 58.21 )
2024-05-31 01:33:05.171107 INFO::Formatting Data.
2024-05-31 01:33:05.171957 INFO::Recognized SummarizedExperiment
2024-05-31 01:33:05.172494 INFO::Typecasting input to dataframe.
2024-05-31 01:33:05.204714 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:05.205905 INFO::Removing potential empty rows and columns
2024-05-31 01:33:05.209699 INFO::Found 0 missing values.
2024-05-31 01:33:05.215362 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:05.215866 INFO::Done
2024-05-31 01:33:05.216327 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:05.219483 INFO::Starting hierarchical adjustment
2024-05-31 01:33:05.220098 INFO::Found 2 batches.
2024-05-31 01:33:05.220556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:05.221515 INFO::Using default BPPARAM
2024-05-31 01:33:05.221982 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:05.22281 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:05.301712 INFO::Done
2024-05-31 01:33:05.302321 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:05.305208 INFO::ASW Batch was 0.00828274940492908 prior to batch effect correction and is now -0.0877324068929086 .
2024-05-31 01:33:05.305949 INFO::Total function execution time is 0.135270833969116 s and adjustment time is 0.0817191600799561 s ( 60.41 )
2024-05-31 01:33:05.320874 INFO::Formatting Data.
2024-05-31 01:33:05.321531 INFO::Recognized SummarizedExperiment
2024-05-31 01:33:05.321976 INFO::Typecasting input to dataframe.
2024-05-31 01:33:05.329571 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:05.330655 INFO::Removing potential empty rows and columns
2024-05-31 01:33:05.333553 INFO::Found 0 missing values.
2024-05-31 01:33:05.339183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:05.339741 INFO::Done
2024-05-31 01:33:05.340213 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:05.343087 INFO::Starting hierarchical adjustment
2024-05-31 01:33:05.343732 INFO::Found 2 batches.
2024-05-31 01:33:05.344176 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:05.344707 INFO::Using default BPPARAM
2024-05-31 01:33:05.345151 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:05.346025 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:05.365905 INFO::Done
2024-05-31 01:33:05.366594 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:05.369676 INFO::ASW Batch was 0.00519684622803398 prior to batch effect correction and is now 0.00519684622803398 .
2024-05-31 01:33:05.370443 INFO::Total function execution time is 0.0495502948760986 s and adjustment time is 0.0222630500793457 s ( 44.93 )
2024-05-31 01:33:05.386398 INFO::Formatting Data.
2024-05-31 01:33:05.387138 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:05.387938 INFO::Removing potential empty rows and columns
2024-05-31 01:33:05.388853 INFO::Found 0 missing values.
2024-05-31 01:33:05.391353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:05.391819 INFO::Done
2024-05-31 01:33:05.392281 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:05.394083 INFO::Starting hierarchical adjustment
2024-05-31 01:33:05.394683 INFO::Found 3 batches.
2024-05-31 01:33:05.395124 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:05.395667 INFO::Using default BPPARAM
2024-05-31 01:33:05.396116 INFO::Processing subtree level 1
2024-05-31 01:33:05.545969 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:33:05.548245 INFO::Done
2024-05-31 01:33:05.549182 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:05.55265 INFO::ASW Batch was 0.055576933386128 prior to batch effect correction and is now -0.16510093117502 .
2024-05-31 01:33:05.554005 INFO::Total function execution time is 0.167535066604614 s and adjustment time is 0.153614044189453 s ( 91.69 )
2024-05-31 01:33:05.574883 INFO::Skipping initial DF formatting
2024-05-31 01:33:05.575866 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:05.582307 INFO::Starting hierarchical adjustment
2024-05-31 01:33:05.583487 INFO::Found 5 batches.
2024-05-31 01:33:05.584344 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:05.58523 INFO::Using default BPPARAM
2024-05-31 01:33:05.586063 INFO::Processing subtree level 1
2024-05-31 01:33:05.749181 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:05.751029 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:05.77316 INFO::Done
2024-05-31 01:33:05.773945 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:05.778489 INFO::ASW Batch was 0.519992900326707 prior to batch effect correction and is now 0.519992900326707 .
2024-05-31 01:33:05.779248 INFO::ASW Label was 0.354206730224389 prior to batch effect correction and is now 0.354206730224389 .
2024-05-31 01:33:05.780231 INFO::Total function execution time is 0.205453634262085 s and adjustment time is 0.189932584762573 s ( 92.45 )
2024-05-31 01:33:05.797857 INFO::Formatting Data.
2024-05-31 01:33:05.798616 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:05.79959 INFO::Removing potential empty rows and columns
2024-05-31 01:33:05.800587 INFO::Found 0 missing values.
2024-05-31 01:33:05.804625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:05.805138 INFO::Done
2024-05-31 01:33:05.805673 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:05.808788 INFO::Starting hierarchical adjustment
2024-05-31 01:33:05.809495 INFO::Found 5 batches.
2024-05-31 01:33:05.810025 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:05.810636 INFO::Using default BPPARAM
2024-05-31 01:33:05.811184 INFO::Processing subtree level 1
2024-05-31 01:33:05.931167 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:05.933391 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:05.956825 INFO::Done
2024-05-31 01:33:05.95778 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:05.962523 INFO::ASW Batch was 0.274694578330711 prior to batch effect correction and is now -0.062543651026024 .
2024-05-31 01:33:05.963402 INFO::ASW Label was 0.413773250311868 prior to batch effect correction and is now 0.802024668632448 .
2024-05-31 01:33:05.964665 INFO::Total function execution time is 0.166786432266235 s and adjustment time is 0.147404909133911 s ( 88.38 )
2024-05-31 01:33:05.96587 INFO::Formatting Data.
2024-05-31 01:33:05.966758 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:05.968014 INFO::Removing potential empty rows and columns
2024-05-31 01:33:05.969448 INFO::Found 0 missing values.
2024-05-31 01:33:05.975655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:05.976492 INFO::Done
2024-05-31 01:33:05.977278 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:05.981632 INFO::Starting hierarchical adjustment
2024-05-31 01:33:05.982677 INFO::Found 5 batches.
2024-05-31 01:33:05.983487 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:05.984406 INFO::Using default BPPARAM
2024-05-31 01:33:05.985212 INFO::Processing subtree level 1
2024-05-31 01:33:06.115827 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:06.118135 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:06.141232 INFO::Done
2024-05-31 01:33:06.142407 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:06.147212 INFO::ASW Batch was 0.274694578330711 prior to batch effect correction and is now -0.062543651026024 .
2024-05-31 01:33:06.148118 INFO::ASW Label was 0.413773250311868 prior to batch effect correction and is now 0.802024668632448 .
2024-05-31 01:33:06.149356 INFO::Total function execution time is 0.183485984802246 s and adjustment time is 0.158707857131958 s ( 86.5 )
2024-05-31 01:33:06.164479 INFO::Formatting Data.
2024-05-31 01:33:06.165262 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:06.166178 INFO::Removing potential empty rows and columns
2024-05-31 01:33:06.167172 INFO::Found 0 missing values.
2024-05-31 01:33:06.171224 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:06.171759 INFO::Done
2024-05-31 01:33:06.172297 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:06.175346 INFO::Starting hierarchical adjustment
2024-05-31 01:33:06.176028 INFO::Found 5 batches.
2024-05-31 01:33:06.176566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:06.177172 INFO::Using default BPPARAM
2024-05-31 01:33:06.177709 INFO::Processing subtree level 1
2024-05-31 01:33:06.293594 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:06.295229 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:06.30968 INFO::Done
2024-05-31 01:33:06.31035 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:06.31346 INFO::ASW Batch was 0.322168241211033 prior to batch effect correction and is now -0.034007923771739 .
2024-05-31 01:33:06.314031 INFO::ASW Label was 0.403470763076702 prior to batch effect correction and is now 0.74967279552613 .
2024-05-31 01:33:06.314776 INFO::Total function execution time is 0.15041184425354 s and adjustment time is 0.133779525756836 s ( 88.94 )
2024-05-31 01:33:06.315549 INFO::Formatting Data.
2024-05-31 01:33:06.316132 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:06.31699 INFO::Removing potential empty rows and columns
2024-05-31 01:33:06.31795 INFO::Found 0 missing values.
2024-05-31 01:33:06.321728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:06.322242 INFO::Done
2024-05-31 01:33:06.322728 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:06.325518 INFO::Starting hierarchical adjustment
2024-05-31 01:33:06.326188 INFO::Found 5 batches.
2024-05-31 01:33:06.326693 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:06.327302 INFO::Using default BPPARAM
2024-05-31 01:33:06.327828 INFO::Processing subtree level 1
2024-05-31 01:33:06.430315 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:06.431763 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:06.44598 INFO::Done
2024-05-31 01:33:06.446644 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:06.449663 INFO::ASW Batch was 0.322168241211033 prior to batch effect correction and is now -0.034007923771739 .
2024-05-31 01:33:06.450233 INFO::ASW Label was 0.403470763076702 prior to batch effect correction and is now 0.74967279552613 .
2024-05-31 01:33:06.45097 INFO::Total function execution time is 0.135422468185425 s and adjustment time is 0.119916200637817 s ( 88.55 )
2024-05-31 01:33:06.463599 INFO::Formatting Data.
2024-05-31 01:33:06.46429 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:06.465138 INFO::Removing potential empty rows and columns
2024-05-31 01:33:06.466073 INFO::Found 0 missing values.
2024-05-31 01:33:06.468601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:06.469128 INFO::Done
2024-05-31 01:33:06.469614 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:06.472412 INFO::Starting hierarchical adjustment
2024-05-31 01:33:06.473074 INFO::Found 2 batches.
2024-05-31 01:33:06.473583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:06.474164 INFO::Using default BPPARAM
2024-05-31 01:33:06.47468 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:06.475523 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:06.489051 INFO::Done
2024-05-31 01:33:06.489669 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:06.492457 INFO::ASW Batch was 0.592269969793217 prior to batch effect correction and is now 0.147670802278246 .
2024-05-31 01:33:06.493007 INFO::ASW Label was 0.556293872403359 prior to batch effect correction and is now 0.815505877511106 .
2024-05-31 01:33:06.49378 INFO::Total function execution time is 0.0302224159240723 s and adjustment time is 0.016103982925415 s ( 53.28 )
2024-05-31 01:33:06.494527 INFO::Formatting Data.
2024-05-31 01:33:06.4951 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:06.495908 INFO::Removing potential empty rows and columns
2024-05-31 01:33:06.496834 INFO::Found 0 missing values.
2024-05-31 01:33:06.499305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:06.499823 INFO::Done
2024-05-31 01:33:06.500318 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:06.503087 INFO::Starting hierarchical adjustment
2024-05-31 01:33:06.503751 INFO::Found 2 batches.
2024-05-31 01:33:06.504262 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:06.504817 INFO::Using default BPPARAM
2024-05-31 01:33:06.505338 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:06.506199 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:06.519966 INFO::Done
2024-05-31 01:33:06.520563 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:06.523243 INFO::ASW Batch was 0.592269969793217 prior to batch effect correction and is now 0.147670802278246 .
2024-05-31 01:33:06.523778 INFO::ASW Label was 0.556293872403359 prior to batch effect correction and is now 0.815505877511106 .
2024-05-31 01:33:06.524544 INFO::Total function execution time is 0.0300281047821045 s and adjustment time is 0.0163612365722656 s ( 54.49 )
2024-05-31 01:33:06.534636 INFO::Formatting Data.
2024-05-31 01:33:06.535323 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:06.536142 INFO::Removing potential empty rows and columns
2024-05-31 01:33:06.536999 INFO::Found 0 missing values.
2024-05-31 01:33:06.538963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:06.539464 INFO::Done
2024-05-31 01:33:06.539995 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:06.541824 INFO::Starting hierarchical adjustment
2024-05-31 01:33:06.542501 INFO::Found 2 batches.
2024-05-31 01:33:06.542996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:06.543576 INFO::Using default BPPARAM
2024-05-31 01:33:06.54406 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:06.544922 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:06.575041 INFO::Done
2024-05-31 01:33:06.575705 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:06.577557 INFO::ASW Batch was 0.29622744697504 prior to batch effect correction and is now -0.170605736279033 .
2024-05-31 01:33:06.578308 INFO::Total function execution time is 0.0437188148498535 s and adjustment time is 0.0326540470123291 s ( 74.69 )
2024-05-31 01:33:06.589078 INFO::Formatting Data.
2024-05-31 01:33:06.58978 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:06.590608 INFO::Removing potential empty rows and columns
2024-05-31 01:33:06.591542 INFO::Found 0 missing values.
2024-05-31 01:33:06.59267 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.
2024-05-31 01:33:06.608975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:06.609704 INFO::Done
2024-05-31 01:33:06.610205 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:06.612941 INFO::Starting hierarchical adjustment
2024-05-31 01:33:06.613595 INFO::Found 2 batches.
2024-05-31 01:33:06.614091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:06.614628 INFO::Using default BPPARAM
2024-05-31 01:33:06.615109 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:06.61601 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:06.63147 INFO::Done
2024-05-31 01:33:06.632049 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:06.634733 INFO::ASW Batch was 0.67425795413732 prior to batch effect correction and is now 0.126504536717236 .
2024-05-31 01:33:06.635234 INFO::ASW Label was 0.390929413028538 prior to batch effect correction and is now 0.769148135316029 .
2024-05-31 01:33:06.63591 INFO::Total function execution time is 0.0468900203704834 s and adjustment time is 0.0179994106292725 s ( 38.39 )
2024-05-31 01:33:06.636625 INFO::Formatting Data.
2024-05-31 01:33:06.637182 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:06.637986 INFO::Removing potential empty rows and columns
2024-05-31 01:33:06.638875 INFO::Found 0 missing values.
2024-05-31 01:33:06.639693 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.
2024-05-31 01:33:06.643951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:06.644464 INFO::Done
2024-05-31 01:33:06.644945 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:06.647673 INFO::Starting hierarchical adjustment
2024-05-31 01:33:06.648331 INFO::Found 2 batches.
2024-05-31 01:33:06.648823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:06.649394 INFO::Using default BPPARAM
2024-05-31 01:33:06.649886 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:06.650766 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:06.666328 INFO::Done
2024-05-31 01:33:06.666903 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:06.669647 INFO::ASW Batch was 0.67425795413732 prior to batch effect correction and is now 0.126504536717236 .
2024-05-31 01:33:06.67018 INFO::ASW Label was 0.390929413028538 prior to batch effect correction and is now 0.769148135316029 .
2024-05-31 01:33:06.670928 INFO::Total function execution time is 0.0343115329742432 s and adjustment time is 0.0181422233581543 s ( 52.88 )
2024-05-31 01:33:06.864135 INFO::Formatting Data.
2024-05-31 01:33:06.865027 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:06.865916 INFO::Removing potential empty rows and columns
2024-05-31 01:33:06.86694 INFO::Found 0 missing values.
2024-05-31 01:33:06.869789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:06.870301 INFO::Done
2024-05-31 01:33:06.870777 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:06.872858 INFO::Starting hierarchical adjustment
2024-05-31 01:33:06.873508 INFO::Found 3 batches.
2024-05-31 01:33:06.873995 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:06.874584 INFO::Using default BPPARAM
2024-05-31 01:33:06.875088 INFO::Processing subtree level 1
2024-05-31 01:33:06.963617 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:33:06.965458 INFO::Done
2024-05-31 01:33:06.966152 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:06.968653 INFO::ASW Batch was -0.119088448948672 prior to batch effect correction and is now -0.119088448948672 .
2024-05-31 01:33:06.969633 INFO::Total function execution time is 0.105758666992188 s and adjustment time is 0.0920412540435791 s ( 87.03 )
2024-05-31 01:33:06.970789 INFO::Formatting Data.
2024-05-31 01:33:06.97145 INFO::Typecasting input to dataframe.
2024-05-31 01:33:06.97223 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:06.973181 INFO::Removing potential empty rows and columns
2024-05-31 01:33:06.97425 INFO::Found 0 missing values.
2024-05-31 01:33:06.977088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:06.977608 INFO::Done
2024-05-31 01:33:06.978086 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:06.980018 INFO::Starting hierarchical adjustment
2024-05-31 01:33:06.980703 INFO::Found 3 batches.
2024-05-31 01:33:06.981214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:06.981813 INFO::Using default BPPARAM
2024-05-31 01:33:06.982314 INFO::Processing subtree level 1
2024-05-31 01:33:07.077382 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:33:07.079131 INFO::Done
2024-05-31 01:33:07.079746 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:07.082069 INFO::ASW Batch was -0.119088448948672 prior to batch effect correction and is now -0.119088448948672 .
2024-05-31 01:33:07.083058 INFO::Total function execution time is 0.112261772155762 s and adjustment time is 0.0985479354858398 s ( 87.78 )
2024-05-31 01:33:07.096068 INFO::Formatting Data.
2024-05-31 01:33:07.096871 INFO::Typecasting input to dataframe.
2024-05-31 01:33:07.097703 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:07.098573 INFO::Removing potential empty rows and columns
2024-05-31 01:33:07.09961 INFO::Found 0 missing values.
2024-05-31 01:33:07.102564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:07.10308 INFO::Done
2024-05-31 01:33:07.103592 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:07.105542 INFO::Starting hierarchical adjustment
2024-05-31 01:33:07.106209 INFO::Found 3 batches.
2024-05-31 01:33:07.106735 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:07.107332 INFO::Using default BPPARAM
2024-05-31 01:33:07.107841 INFO::Processing subtree level 1
2024-05-31 01:33:07.195215 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:33:07.196837 INFO::Done
2024-05-31 01:33:07.197417 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:07.199692 INFO::ASW Batch was -0.107093208337371 prior to batch effect correction and is now -0.107093208337371 .
2024-05-31 01:33:07.2006 INFO::Total function execution time is 0.104588747024536 s and adjustment time is 0.0907552242279053 s ( 86.77 )
2024-05-31 01:33:07.3353 INFO::Formatting Data.
2024-05-31 01:33:07.33607 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:07.337163 INFO::Removing potential empty rows and columns
2024-05-31 01:33:07.339766 INFO::Found 1000 missing values.
2024-05-31 01:33:07.357438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:07.358305 INFO::Done
2024-05-31 01:33:07.358894 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:07.36457 INFO::Starting hierarchical adjustment
2024-05-31 01:33:07.365344 INFO::Found 10 batches.
2024-05-31 01:33:07.365867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:07.366484 INFO::Using default BPPARAM
2024-05-31 01:33:07.367014 INFO::Processing subtree level 1
2024-05-31 01:33:07.49606 INFO::Processing subtree level 2
2024-05-31 01:33:07.710341 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:33:07.712507 INFO::Done
2024-05-31 01:33:07.713306 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:07.719941 INFO::ASW Batch was 0.507225725557186 prior to batch effect correction and is now 0.507225725557186 .
2024-05-31 01:33:07.720747 INFO::ASW Label was 0.309912976500915 prior to batch effect correction and is now 0.309912976500915 .
2024-05-31 01:33:07.721817 INFO::Total function execution time is 0.386544466018677 s and adjustment time is 0.347283601760864 s ( 89.84 )
2024-05-31 01:33:07.722817 INFO::Formatting Data.
2024-05-31 01:33:07.723595 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:07.724958 INFO::Removing potential empty rows and columns
2024-05-31 01:33:07.728337 INFO::Found 1000 missing values.
2024-05-31 01:33:07.750124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:07.750974 INFO::Done
2024-05-31 01:33:07.751634 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:07.758084 INFO::Starting hierarchical adjustment
2024-05-31 01:33:07.758913 INFO::Found 10 batches.
2024-05-31 01:33:08.812219 INFO::Set up parallel execution backend with 2 workers
2024-05-31 01:33:08.813382 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-31 01:33:09.886705 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:33:09.888597 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:33:09.904871 INFO::Done
2024-05-31 01:33:09.9055 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:09.910217 INFO::ASW Batch was 0.507225725557186 prior to batch effect correction and is now 0.507225725557186 .
2024-05-31 01:33:09.910753 INFO::ASW Label was 0.309912976500915 prior to batch effect correction and is now 0.309912976500915 .
2024-05-31 01:33:09.911527 INFO::Total function execution time is 2.18878364562988 s and adjustment time is 2.14612793922424 s ( 98.05 )
2024-05-31 01:33:10.038935 INFO::Formatting Data.
2024-05-31 01:33:10.039769 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.040737 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.041752 INFO::Found 0 missing values.
2024-05-31 01:33:10.045223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.045777 INFO::Done
2024-05-31 01:33:10.046268 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:33:10.048908 INFO::Starting hierarchical adjustment
2024-05-31 01:33:10.04956 INFO::Found 3 batches.
2024-05-31 01:33:10.050044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:33:10.050617 INFO::Using default BPPARAM
2024-05-31 01:33:10.051108 INFO::Processing subtree level 1
2024-05-31 01:33:10.152363 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:33:10.154133 INFO::Done
2024-05-31 01:33:10.154747 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:33:10.157791 INFO::ASW Batch was 0.260917940453482 prior to batch effect correction and is now -0.118146058294319 .
2024-05-31 01:33:10.158387 INFO::ASW Label was -0.212366103059765 prior to batch effect correction and is now -0.00152314171543526 .
2024-05-31 01:33:10.159255 INFO::Total function execution time is 0.120333671569824 s and adjustment time is 0.104671239852905 s ( 86.98 )
2024-05-31 01:33:10.26564 INFO::Formatting Data.
2024-05-31 01:33:10.266428 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.267288 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.268251 INFO::Found 2 missing values.
2024-05-31 01:33:10.270838 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.271317 INFO::Done
2024-05-31 01:33:10.295193 INFO::Found NA in Reference column
2024-05-31 01:33:10.303884 INFO::Require at least two references per batch.
2024-05-31 01:33:10.323273 INFO::Formatting Data.
2024-05-31 01:33:10.324013 INFO::Recognized SummarizedExperiment
2024-05-31 01:33:10.324535 INFO::Typecasting input to dataframe.
2024-05-31 01:33:10.333896 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.33494 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.338149 INFO::Found 0 missing values.
2024-05-31 01:33:10.344177 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.344737 INFO::Done
2024-05-31 01:33:10.35884 INFO::Formatting Data.
2024-05-31 01:33:10.359559 INFO::Recognized SummarizedExperiment
2024-05-31 01:33:10.360065 INFO::Typecasting input to dataframe.
2024-05-31 01:33:10.376221 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.377362 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.380633 INFO::Found 0 missing values.
2024-05-31 01:33:10.3908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.391471 INFO::Done
2024-05-31 01:33:10.405988 INFO::Formatting Data.
2024-05-31 01:33:10.406683 INFO::Recognized SummarizedExperiment
2024-05-31 01:33:10.407195 INFO::Typecasting input to dataframe.
2024-05-31 01:33:10.423218 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.42427 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.425454 INFO::Found 0 missing values.
2024-05-31 01:33:10.426364 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.
2024-05-31 01:33:10.430618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.431184 INFO::Done
2024-05-31 01:33:10.440912 INFO::Formatting Data.
2024-05-31 01:33:10.441635 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.442466 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.443558 INFO::Found 0 missing values.
2024-05-31 01:33:10.446402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.446898 INFO::Done
2024-05-31 01:33:10.457635 INFO::Formatting Data.
2024-05-31 01:33:10.458358 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.459224 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.460229 INFO::Found 0 missing values.
2024-05-31 01:33:10.462991 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.463532 INFO::Done
2024-05-31 01:33:10.491148 INFO::Formatting Data.
2024-05-31 01:33:10.492013 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.493045 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.494107 INFO::Found 1 missing values.
2024-05-31 01:33:10.496606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.497125 INFO::Done
2024-05-31 01:33:10.513675 INFO::Formatting Data.
2024-05-31 01:33:10.514446 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.515252 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.516116 INFO::Found 2 missing values.
2024-05-31 01:33:10.516974 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.
2024-05-31 01:33:10.51901 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.519531 INFO::Done
2024-05-31 01:33:10.528183 INFO::Formatting Data.
2024-05-31 01:33:10.528868 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.529691 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.530553 INFO::Found 2 missing values.
2024-05-31 01:33:10.532028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.53253 INFO::Done
2024-05-31 01:33:10.542046 INFO::Formatting Data.
2024-05-31 01:33:10.542761 INFO::Typecasting input to dataframe.
2024-05-31 01:33:10.543553 INFO::Replacing NaNs with NAs.
2024-05-31 01:33:10.544371 INFO::Removing potential empty rows and columns
2024-05-31 01:33:10.54528 INFO::Found 0 missing values.
2024-05-31 01:33:10.547953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:33:10.548482 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.002 3.339 19.063
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 22.714 | 1.083 | 16.377 | |
| compute_asw | 0.025 | 0.000 | 0.025 | |
| count_existing | 0.011 | 0.004 | 0.015 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |