Yannis Schumann
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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 2024-10-18 20:39 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-10-16 23:08:00 -0400 (Wed, 16 Oct 2024) |
| EndedAt: 2024-10-16 23:10:09 -0400 (Wed, 16 Oct 2024) |
| EllapsedTime: 129.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.0.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BERT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 8.06 0.61 17.26
* 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: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'BERT' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-10-16 23:09:00.071002 INFO::Formatting Data.
2024-10-16 23:09:00.073949 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:00.088093 INFO::Removing potential empty rows and columns
2024-10-16 23:09:00.340965 INFO::Found 0 missing values.
2024-10-16 23:09:00.344408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:00.345288 INFO::Done
2024-10-16 23:09:00.346007 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:00.359969 INFO::Starting hierarchical adjustment
2024-10-16 23:09:00.360986 INFO::Found 3 batches.
2024-10-16 23:09:00.361693 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:00.362912 INFO::Using default BPPARAM
2024-10-16 23:09:00.363659 INFO::Processing subtree level 1
2024-10-16 23:09:02.746741 INFO::Adjusting the last 1 batches sequentially
2024-10-16 23:09:02.748871 INFO::Done
2024-10-16 23:09:02.750064 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:02.752983 INFO::ASW Batch was 0.0190711358717707 prior to batch effect correction and is now 0.0190711358717707 .
2024-10-16 23:09:02.754514 INFO::Total function execution time is 2.68431305885315 s and adjustment time is 2.38801193237305 s ( 88.96 )
2024-10-16 23:09:02.776142 INFO::Formatting Data.
2024-10-16 23:09:02.7771 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:02.778198 INFO::Removing potential empty rows and columns
2024-10-16 23:09:02.779409 INFO::Found 0 missing values.
2024-10-16 23:09:02.780462 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.
2024-10-16 23:09:02.789407 INFO::Formatting Data.
2024-10-16 23:09:02.790377 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:02.791575 INFO::Removing potential empty rows and columns
2024-10-16 23:09:02.792674 INFO::Found 0 missing values.
2024-10-16 23:09:02.793692 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.
2024-10-16 23:09:02.809711 INFO::Formatting Data.
2024-10-16 23:09:02.810626 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:02.811626 INFO::Removing potential empty rows and columns
2024-10-16 23:09:02.81269 INFO::Found 0 missing values.
2024-10-16 23:09:02.813704 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.
2024-10-16 23:09:02.817254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:02.81795 INFO::Done
2024-10-16 23:09:02.818604 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:02.82058 INFO::Starting hierarchical adjustment
2024-10-16 23:09:02.821396 INFO::Found 2 batches.
2024-10-16 23:09:02.822136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:02.822884 INFO::Using default BPPARAM
2024-10-16 23:09:02.823537 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:02.824576 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:02.840629 INFO::Done
2024-10-16 23:09:02.841483 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:02.843666 INFO::ASW Batch was 0.0168589134654234 prior to batch effect correction and is now -0.11780843641742 .
2024-10-16 23:09:02.84462 INFO::Total function execution time is 0.0349910259246826 s and adjustment time is 0.0193138122558594 s ( 55.2 )
2024-10-16 23:09:02.847362 INFO::Formatting Data.
2024-10-16 23:09:02.848133 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:02.855126 INFO::Formatting Data.
2024-10-16 23:09:02.85599 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:02.856992 INFO::Removing potential empty rows and columns
2024-10-16 23:09:02.858053 INFO::Found 0 missing values.
2024-10-16 23:09:02.860431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:02.861106 INFO::Done
2024-10-16 23:09:02.861757 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:02.863764 INFO::Starting hierarchical adjustment
2024-10-16 23:09:02.864626 INFO::Found 2 batches.
2024-10-16 23:09:02.865293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:02.866016 INFO::Using default BPPARAM
2024-10-16 23:09:02.866668 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:02.867689 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:02.879571 INFO::Done
2024-10-16 23:09:02.880456 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:02.882501 INFO::ASW Batch was -0.0425104802113105 prior to batch effect correction and is now -0.117885274786247 .
2024-10-16 23:09:02.883447 INFO::Total function execution time is 0.028357982635498 s and adjustment time is 0.0150551795959473 s ( 53.09 )
2024-10-16 23:09:02.884622 INFO::Formatting Data.
2024-10-16 23:09:02.885383 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:02.886372 INFO::Removing potential empty rows and columns
2024-10-16 23:09:02.887438 INFO::Found 0 missing values.
2024-10-16 23:09:02.889882 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:02.890549 INFO::Done
2024-10-16 23:09:02.891191 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:02.893203 INFO::Starting hierarchical adjustment
2024-10-16 23:09:02.894025 INFO::Found 2 batches.
2024-10-16 23:09:02.894692 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:02.895444 INFO::Using default BPPARAM
2024-10-16 23:09:02.896104 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:02.89711 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:02.909115 INFO::Done
2024-10-16 23:09:02.909944 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:02.91207 INFO::ASW Batch was -0.0425104802113105 prior to batch effect correction and is now -0.117885274786247 .
2024-10-16 23:09:02.913036 INFO::Total function execution time is 0.0284199714660645 s and adjustment time is 0.0151910781860352 s ( 53.45 )
2024-10-16 23:09:04.885536 INFO::Formatting Data.
2024-10-16 23:09:04.886439 INFO::Recognized SummarizedExperiment
2024-10-16 23:09:04.887156 INFO::Typecasting input to dataframe.
2024-10-16 23:09:04.91766 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:04.919107 INFO::Removing potential empty rows and columns
2024-10-16 23:09:04.922203 INFO::Found 0 missing values.
2024-10-16 23:09:04.927818 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:04.928668 INFO::Done
2024-10-16 23:09:04.929387 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:04.932973 INFO::Starting hierarchical adjustment
2024-10-16 23:09:04.933816 INFO::Found 2 batches.
2024-10-16 23:09:04.934484 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:04.935708 INFO::Using default BPPARAM
2024-10-16 23:09:04.936395 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:04.937549 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:04.979409 INFO::Done
2024-10-16 23:09:04.980269 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:04.983973 INFO::ASW Batch was -0.0129900169363084 prior to batch effect correction and is now -0.0908716810399709 .
2024-10-16 23:09:04.984989 INFO::Total function execution time is 0.0997378826141357 s and adjustment time is 0.0456879138946533 s ( 45.81 )
2024-10-16 23:09:05.688882 INFO::Formatting Data.
2024-10-16 23:09:05.689819 INFO::Recognized SummarizedExperiment
2024-10-16 23:09:05.690564 INFO::Typecasting input to dataframe.
2024-10-16 23:09:05.698876 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:05.700325 INFO::Removing potential empty rows and columns
2024-10-16 23:09:05.703106 INFO::Found 0 missing values.
2024-10-16 23:09:05.708569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:05.70936 INFO::Done
2024-10-16 23:09:05.710119 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:05.713658 INFO::Starting hierarchical adjustment
2024-10-16 23:09:05.714494 INFO::Found 2 batches.
2024-10-16 23:09:05.715189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:05.715974 INFO::Using default BPPARAM
2024-10-16 23:09:05.716633 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:05.717794 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:05.73567 INFO::Done
2024-10-16 23:09:05.736556 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:05.740273 INFO::ASW Batch was 0.00422385782366042 prior to batch effect correction and is now 0.00422385782366042 .
2024-10-16 23:09:05.741417 INFO::Total function execution time is 0.0525059700012207 s and adjustment time is 0.021265983581543 s ( 40.5 )
2024-10-16 23:09:05.762459 INFO::Formatting Data.
2024-10-16 23:09:05.763377 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:05.764387 INFO::Removing potential empty rows and columns
2024-10-16 23:09:05.765443 INFO::Found 0 missing values.
2024-10-16 23:09:05.768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:05.768687 INFO::Done
2024-10-16 23:09:05.769348 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:05.771334 INFO::Starting hierarchical adjustment
2024-10-16 23:09:05.772182 INFO::Found 3 batches.
2024-10-16 23:09:05.772856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:05.773598 INFO::Using default BPPARAM
2024-10-16 23:09:05.774251 INFO::Processing subtree level 1
2024-10-16 23:09:15.67484 INFO::Adjusting the last 1 batches sequentially
2024-10-16 23:09:15.677092 INFO::Done
2024-10-16 23:09:15.678337 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:15.681557 INFO::ASW Batch was -0.0561538030748538 prior to batch effect correction and is now -0.173853662995518 .
2024-10-16 23:09:15.683099 INFO::Total function execution time is 9.92062091827393 s and adjustment time is 9.90497899055481 s ( 99.84 )
2024-10-16 23:09:15.706971 INFO::Skipping initial DF formatting
2024-10-16 23:09:15.708347 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:15.715012 INFO::Starting hierarchical adjustment
2024-10-16 23:09:15.716557 INFO::Found 5 batches.
2024-10-16 23:09:15.717715 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:15.718977 INFO::Using default BPPARAM
2024-10-16 23:09:15.720097 INFO::Processing subtree level 1
2024-10-16 23:09:18.585724 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:18.587438 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:18.608342 INFO::Done
2024-10-16 23:09:18.609632 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:18.615616 INFO::ASW Batch was 0.503012543407577 prior to batch effect correction and is now 0.503012543407577 .
2024-10-16 23:09:18.616434 INFO::ASW Label was 0.402966958108701 prior to batch effect correction and is now 0.402966958108701 .
2024-10-16 23:09:18.617407 INFO::Total function execution time is 2.91063690185547 s and adjustment time is 2.89200305938721 s ( 99.36 )
2024-10-16 23:09:18.635102 INFO::Formatting Data.
2024-10-16 23:09:18.63624 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:18.637317 INFO::Removing potential empty rows and columns
2024-10-16 23:09:18.638406 INFO::Found 0 missing values.
2024-10-16 23:09:18.641723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:18.642391 INFO::Done
2024-10-16 23:09:18.643034 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:18.645965 INFO::Starting hierarchical adjustment
2024-10-16 23:09:18.646787 INFO::Found 5 batches.
2024-10-16 23:09:18.647449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:18.648177 INFO::Using default BPPARAM
2024-10-16 23:09:18.648838 INFO::Processing subtree level 1
2024-10-16 23:09:21.692295 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:21.694323 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:21.712686 INFO::Done
2024-10-16 23:09:21.714003 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:21.718602 INFO::ASW Batch was 0.622122434370743 prior to batch effect correction and is now -0.0661300947181087 .
2024-10-16 23:09:21.719811 INFO::ASW Label was 0.0694595707117401 prior to batch effect correction and is now 0.778396540293654 .
2024-10-16 23:09:21.721277 INFO::Total function execution time is 3.08622789382935 s and adjustment time is 3.0659511089325 s ( 99.34 )
2024-10-16 23:09:21.722734 INFO::Formatting Data.
2024-10-16 23:09:21.723943 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:21.725543 INFO::Removing potential empty rows and columns
2024-10-16 23:09:21.727195 INFO::Found 0 missing values.
2024-10-16 23:09:21.732399 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:21.733447 INFO::Done
2024-10-16 23:09:21.734471 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:21.738727 INFO::Starting hierarchical adjustment
2024-10-16 23:09:21.739941 INFO::Found 5 batches.
2024-10-16 23:09:21.740611 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:21.741329 INFO::Using default BPPARAM
2024-10-16 23:09:21.741981 INFO::Processing subtree level 1
2024-10-16 23:09:24.763148 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:24.765083 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:24.781491 INFO::Done
2024-10-16 23:09:24.782681 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:24.786859 INFO::ASW Batch was 0.622122434370743 prior to batch effect correction and is now -0.0661300947181087 .
2024-10-16 23:09:24.788026 INFO::ASW Label was 0.0694595707117401 prior to batch effect correction and is now 0.778396540293654 .
2024-10-16 23:09:24.789351 INFO::Total function execution time is 3.06668210029602 s and adjustment time is 3.04163002967834 s ( 99.18 )
2024-10-16 23:09:24.808913 INFO::Formatting Data.
2024-10-16 23:09:24.810312 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:24.811391 INFO::Removing potential empty rows and columns
2024-10-16 23:09:24.812616 INFO::Found 0 missing values.
2024-10-16 23:09:24.817896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:24.819094 INFO::Done
2024-10-16 23:09:24.820261 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:24.825118 INFO::Starting hierarchical adjustment
2024-10-16 23:09:24.825987 INFO::Found 5 batches.
2024-10-16 23:09:24.82666 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:24.827392 INFO::Using default BPPARAM
2024-10-16 23:09:24.828091 INFO::Processing subtree level 1
2024-10-16 23:09:27.775901 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:27.777946 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:27.798311 INFO::Done
2024-10-16 23:09:27.79978 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:27.804856 INFO::ASW Batch was 0.570003613430586 prior to batch effect correction and is now -0.0391154929940994 .
2024-10-16 23:09:27.806256 INFO::ASW Label was 0.272910641706381 prior to batch effect correction and is now 0.658785871194688 .
2024-10-16 23:09:27.807777 INFO::Total function execution time is 2.99893999099731 s and adjustment time is 2.97235417366028 s ( 99.11 )
2024-10-16 23:09:27.809236 INFO::Formatting Data.
2024-10-16 23:09:27.810457 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:27.812038 INFO::Removing potential empty rows and columns
2024-10-16 23:09:27.813738 INFO::Found 0 missing values.
2024-10-16 23:09:27.819801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:27.820974 INFO::Done
2024-10-16 23:09:27.822116 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:27.826726 INFO::Starting hierarchical adjustment
2024-10-16 23:09:27.828044 INFO::Found 5 batches.
2024-10-16 23:09:27.829111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:27.830281 INFO::Using default BPPARAM
2024-10-16 23:09:27.831372 INFO::Processing subtree level 1
2024-10-16 23:09:31.121199 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:31.123117 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:31.135615 INFO::Done
2024-10-16 23:09:31.136472 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:31.139486 INFO::ASW Batch was 0.570003613430586 prior to batch effect correction and is now -0.0391154929940994 .
2024-10-16 23:09:31.140261 INFO::ASW Label was 0.272910641706381 prior to batch effect correction and is now 0.658785871194688 .
2024-10-16 23:09:31.141163 INFO::Total function execution time is 3.33202695846558 s and adjustment time is 3.30775713920593 s ( 99.27 )
2024-10-16 23:09:31.158203 INFO::Formatting Data.
2024-10-16 23:09:31.159601 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:31.161245 INFO::Removing potential empty rows and columns
2024-10-16 23:09:31.163022 INFO::Found 0 missing values.
2024-10-16 23:09:31.166853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:31.168039 INFO::Done
2024-10-16 23:09:31.169188 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:31.173889 INFO::Starting hierarchical adjustment
2024-10-16 23:09:31.175249 INFO::Found 2 batches.
2024-10-16 23:09:31.176427 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:31.177583 INFO::Using default BPPARAM
2024-10-16 23:09:31.178662 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:31.180355 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:31.19924 INFO::Done
2024-10-16 23:09:31.200599 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:31.205031 INFO::ASW Batch was 0.758598709155362 prior to batch effect correction and is now 0.050619328310191 .
2024-10-16 23:09:31.206322 INFO::ASW Label was 0.300957454134395 prior to batch effect correction and is now 0.868316933918368 .
2024-10-16 23:09:31.207869 INFO::Total function execution time is 0.0497550964355469 s and adjustment time is 0.0241410732269287 s ( 48.52 )
2024-10-16 23:09:31.209393 INFO::Formatting Data.
2024-10-16 23:09:31.210698 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:31.212317 INFO::Removing potential empty rows and columns
2024-10-16 23:09:31.213855 INFO::Found 0 missing values.
2024-10-16 23:09:31.217523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:31.218662 INFO::Done
2024-10-16 23:09:31.219818 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:31.224137 INFO::Starting hierarchical adjustment
2024-10-16 23:09:31.22551 INFO::Found 2 batches.
2024-10-16 23:09:31.226655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:31.227905 INFO::Using default BPPARAM
2024-10-16 23:09:31.22906 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:31.230808 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:31.249892 INFO::Done
2024-10-16 23:09:31.251304 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:31.255996 INFO::ASW Batch was 0.758598709155362 prior to batch effect correction and is now 0.050619328310191 .
2024-10-16 23:09:31.257066 INFO::ASW Label was 0.300957454134395 prior to batch effect correction and is now 0.868316933918368 .
2024-10-16 23:09:31.258022 INFO::Total function execution time is 0.0487189292907715 s and adjustment time is 0.0245561599731445 s ( 50.4 )
2024-10-16 23:09:31.27295 INFO::Formatting Data.
2024-10-16 23:09:31.273951 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:31.275096 INFO::Removing potential empty rows and columns
2024-10-16 23:09:31.276233 INFO::Found 0 missing values.
2024-10-16 23:09:31.278405 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:31.279132 INFO::Done
2024-10-16 23:09:31.279803 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:31.281864 INFO::Starting hierarchical adjustment
2024-10-16 23:09:31.282747 INFO::Found 2 batches.
2024-10-16 23:09:31.283423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:31.284153 INFO::Using default BPPARAM
2024-10-16 23:09:31.2848 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:31.285836 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:31.311887 INFO::Done
2024-10-16 23:09:31.312817 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:31.314922 INFO::ASW Batch was -0.0693784392745893 prior to batch effect correction and is now -0.0996519356696529 .
2024-10-16 23:09:31.315889 INFO::Total function execution time is 0.04305100440979 s and adjustment time is 0.0292479991912842 s ( 67.94 )
2024-10-16 23:09:31.331639 INFO::Formatting Data.
2024-10-16 23:09:31.332564 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:31.333621 INFO::Removing potential empty rows and columns
2024-10-16 23:09:31.334796 INFO::Found 0 missing values.
2024-10-16 23:09:31.336149 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.
2024-10-16 23:09:31.340208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:31.340987 INFO::Done
2024-10-16 23:09:31.341675 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:31.344707 INFO::Starting hierarchical adjustment
2024-10-16 23:09:31.345589 INFO::Found 2 batches.
2024-10-16 23:09:31.346292 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:31.347043 INFO::Using default BPPARAM
2024-10-16 23:09:31.347735 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:31.348835 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:31.362762 INFO::Done
2024-10-16 23:09:31.363592 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:31.366529 INFO::ASW Batch was 0.703912278667283 prior to batch effect correction and is now 0.0132113392315987 .
2024-10-16 23:09:31.367267 INFO::ASW Label was 0.362795471219535 prior to batch effect correction and is now 0.871684166607119 .
2024-10-16 23:09:31.368178 INFO::Total function execution time is 0.0366380214691162 s and adjustment time is 0.0172820091247559 s ( 47.17 )
2024-10-16 23:09:31.369104 INFO::Formatting Data.
2024-10-16 23:09:31.369839 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:31.370856 INFO::Removing potential empty rows and columns
2024-10-16 23:09:31.372012 INFO::Found 0 missing values.
2024-10-16 23:09:31.373048 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.
2024-10-16 23:09:31.377035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:31.37774 INFO::Done
2024-10-16 23:09:31.378436 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:31.381372 INFO::Starting hierarchical adjustment
2024-10-16 23:09:31.382273 INFO::Found 2 batches.
2024-10-16 23:09:31.38295 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:31.383714 INFO::Using default BPPARAM
2024-10-16 23:09:31.384411 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:31.385536 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:31.400161 INFO::Done
2024-10-16 23:09:31.401067 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:31.404333 INFO::ASW Batch was 0.703912278667283 prior to batch effect correction and is now 0.0132113392315987 .
2024-10-16 23:09:31.405154 INFO::ASW Label was 0.362795471219535 prior to batch effect correction and is now 0.871684166607119 .
2024-10-16 23:09:31.406184 INFO::Total function execution time is 0.0370678901672363 s and adjustment time is 0.017982006072998 s ( 48.51 )
2024-10-16 23:09:31.616535 INFO::Formatting Data.
2024-10-16 23:09:31.617567 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:31.618798 INFO::Removing potential empty rows and columns
2024-10-16 23:09:31.620038 INFO::Found 0 missing values.
2024-10-16 23:09:31.623088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:31.623833 INFO::Done
2024-10-16 23:09:31.62455 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:31.626841 INFO::Starting hierarchical adjustment
2024-10-16 23:09:31.627745 INFO::Found 3 batches.
2024-10-16 23:09:31.62847 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:31.629326 INFO::Using default BPPARAM
2024-10-16 23:09:31.630077 INFO::Processing subtree level 1
2024-10-16 23:09:34.803272 INFO::Adjusting the last 1 batches sequentially
2024-10-16 23:09:34.805411 INFO::Done
2024-10-16 23:09:34.806663 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:34.809664 INFO::ASW Batch was -0.0620418311916399 prior to batch effect correction and is now -0.0620418311916399 .
2024-10-16 23:09:34.811153 INFO::Total function execution time is 3.19466090202332 s and adjustment time is 3.17775583267212 s ( 99.47 )
2024-10-16 23:09:34.812718 INFO::Formatting Data.
2024-10-16 23:09:34.813844 INFO::Typecasting input to dataframe.
2024-10-16 23:09:34.815156 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:34.816626 INFO::Removing potential empty rows and columns
2024-10-16 23:09:34.818209 INFO::Found 0 missing values.
2024-10-16 23:09:34.822169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:34.823036 INFO::Done
2024-10-16 23:09:34.823704 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:34.825734 INFO::Starting hierarchical adjustment
2024-10-16 23:09:34.826614 INFO::Found 3 batches.
2024-10-16 23:09:34.82728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:34.828077 INFO::Using default BPPARAM
2024-10-16 23:09:34.828748 INFO::Processing subtree level 1
2024-10-16 23:09:37.6746 INFO::Adjusting the last 1 batches sequentially
2024-10-16 23:09:37.676671 INFO::Done
2024-10-16 23:09:37.677862 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:37.680698 INFO::ASW Batch was -0.0620418311916399 prior to batch effect correction and is now -0.0620418311916399 .
2024-10-16 23:09:37.682039 INFO::Total function execution time is 2.86934185028076 s and adjustment time is 2.85014796257019 s ( 99.33 )
2024-10-16 23:09:37.699987 INFO::Formatting Data.
2024-10-16 23:09:37.701285 INFO::Typecasting input to dataframe.
2024-10-16 23:09:37.702716 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:37.704234 INFO::Removing potential empty rows and columns
2024-10-16 23:09:37.705831 INFO::Found 0 missing values.
2024-10-16 23:09:37.709604 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:37.71067 INFO::Done
2024-10-16 23:09:37.711711 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:37.714562 INFO::Starting hierarchical adjustment
2024-10-16 23:09:37.715816 INFO::Found 3 batches.
2024-10-16 23:09:37.716864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:37.718001 INFO::Using default BPPARAM
2024-10-16 23:09:37.719079 INFO::Processing subtree level 1
2024-10-16 23:09:40.776384 INFO::Adjusting the last 1 batches sequentially
2024-10-16 23:09:40.778506 INFO::Done
2024-10-16 23:09:40.779697 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:40.782574 INFO::ASW Batch was -0.0464355801551562 prior to batch effect correction and is now -0.0464355801551562 .
2024-10-16 23:09:40.783924 INFO::Total function execution time is 3.08397912979126 s and adjustment time is 3.06284809112549 s ( 99.31 )
2024-10-16 23:09:43.793797 INFO::Formatting Data.
2024-10-16 23:09:43.795269 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:43.796566 INFO::Removing potential empty rows and columns
2024-10-16 23:09:43.798827 INFO::Found 1000 missing values.
2024-10-16 23:09:43.815073 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:43.81615 INFO::Done
2024-10-16 23:09:43.816909 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:43.82566 INFO::Starting hierarchical adjustment
2024-10-16 23:09:43.82719 INFO::Found 10 batches.
2024-10-16 23:09:43.828339 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:43.82954 INFO::Using default BPPARAM
2024-10-16 23:09:43.830642 INFO::Processing subtree level 1
2024-10-16 23:09:46.838464 INFO::Processing subtree level 2
2024-10-16 23:09:49.725456 INFO::Adjusting the last 1 batches sequentially
2024-10-16 23:09:49.727762 INFO::Done
2024-10-16 23:09:49.729024 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:49.737927 INFO::ASW Batch was 0.492018322486443 prior to batch effect correction and is now 0.492018322486443 .
2024-10-16 23:09:49.739247 INFO::ASW Label was 0.356067657205009 prior to batch effect correction and is now 0.356067657205009 .
2024-10-16 23:09:49.740835 INFO::Total function execution time is 5.94717192649841 s and adjustment time is 5.90078592300415 s ( 99.22 )
2024-10-16 23:09:49.742239 INFO::Formatting Data.
2024-10-16 23:09:49.743461 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:49.745269 INFO::Removing potential empty rows and columns
2024-10-16 23:09:49.748871 INFO::Found 1000 missing values.
2024-10-16 23:09:49.771369 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:49.772778 INFO::Done
2024-10-16 23:09:49.774002 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:49.78358 INFO::Starting hierarchical adjustment
2024-10-16 23:09:49.785169 INFO::Found 10 batches.
2024-10-16 23:09:50.47728 INFO::Set up parallel execution backend with 2 workers
2024-10-16 23:09:50.478228 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-16 23:09:53.422756 INFO::Adjusting the last 2 batches sequentially
2024-10-16 23:09:53.424192 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-16 23:09:53.438153 INFO::Done
2024-10-16 23:09:53.439041 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:53.444682 INFO::ASW Batch was 0.492018322486443 prior to batch effect correction and is now 0.492018322486443 .
2024-10-16 23:09:53.445473 INFO::ASW Label was 0.356067657205009 prior to batch effect correction and is now 0.356067657205009 .
2024-10-16 23:09:53.446423 INFO::Total function execution time is 3.70424914360046 s and adjustment time is 3.65327286720276 s ( 98.62 )
2024-10-16 23:09:56.198508 INFO::Formatting Data.
2024-10-16 23:09:56.199482 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:56.200553 INFO::Removing potential empty rows and columns
2024-10-16 23:09:56.20166 INFO::Found 0 missing values.
2024-10-16 23:09:56.204718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:56.205807 INFO::Done
2024-10-16 23:09:56.206953 INFO::Acquiring quality metrics before batch effect correction.
2024-10-16 23:09:56.2113 INFO::Starting hierarchical adjustment
2024-10-16 23:09:56.212687 INFO::Found 3 batches.
2024-10-16 23:09:56.213832 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-16 23:09:56.215062 INFO::Using default BPPARAM
2024-10-16 23:09:56.216191 INFO::Processing subtree level 1
2024-10-16 23:09:59.141616 INFO::Adjusting the last 1 batches sequentially
2024-10-16 23:09:59.143179 INFO::Done
2024-10-16 23:09:59.144176 INFO::Acquiring quality metrics after batch effect correction.
2024-10-16 23:09:59.148477 INFO::ASW Batch was 0.201487647898124 prior to batch effect correction and is now -0.158552260500858 .
2024-10-16 23:09:59.149317 INFO::ASW Label was -0.180420456600275 prior to batch effect correction and is now 0.0713106553805594 .
2024-10-16 23:09:59.150247 INFO::Total function execution time is 2.95185303688049 s and adjustment time is 2.93075513839722 s ( 99.29 )
2024-10-16 23:09:59.288978 INFO::Formatting Data.
2024-10-16 23:09:59.289959 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:59.291072 INFO::Removing potential empty rows and columns
2024-10-16 23:09:59.29229 INFO::Found 2 missing values.
2024-10-16 23:09:59.294744 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:59.295431 INFO::Done
2024-10-16 23:09:59.339241 INFO::Found NA in Reference column
2024-10-16 23:09:59.356148 INFO::Require at least two references per batch.
2024-10-16 23:09:59.389335 INFO::Formatting Data.
2024-10-16 23:09:59.390803 INFO::Recognized SummarizedExperiment
2024-10-16 23:09:59.392029 INFO::Typecasting input to dataframe.
2024-10-16 23:09:59.401783 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:59.403042 INFO::Removing potential empty rows and columns
2024-10-16 23:09:59.405674 INFO::Found 0 missing values.
2024-10-16 23:09:59.412278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:59.413446 INFO::Done
2024-10-16 23:09:59.431365 INFO::Formatting Data.
2024-10-16 23:09:59.432738 INFO::Recognized SummarizedExperiment
2024-10-16 23:09:59.433552 INFO::Typecasting input to dataframe.
2024-10-16 23:09:59.453849 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:59.455952 INFO::Removing potential empty rows and columns
2024-10-16 23:09:59.459408 INFO::Found 0 missing values.
2024-10-16 23:09:59.467166 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:59.46796 INFO::Done
2024-10-16 23:09:59.482293 INFO::Formatting Data.
2024-10-16 23:09:59.483208 INFO::Recognized SummarizedExperiment
2024-10-16 23:09:59.483906 INFO::Typecasting input to dataframe.
2024-10-16 23:09:59.502261 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:59.503952 INFO::Removing potential empty rows and columns
2024-10-16 23:09:59.505641 INFO::Found 0 missing values.
2024-10-16 23:09:59.507182 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.
2024-10-16 23:09:59.512498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:59.513583 INFO::Done
2024-10-16 23:09:59.531599 INFO::Formatting Data.
2024-10-16 23:09:59.532964 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:59.534467 INFO::Removing potential empty rows and columns
2024-10-16 23:09:59.536045 INFO::Found 0 missing values.
2024-10-16 23:09:59.539693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:59.540741 INFO::Done
2024-10-16 23:09:59.559781 INFO::Formatting Data.
2024-10-16 23:09:59.561136 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:59.562718 INFO::Removing potential empty rows and columns
2024-10-16 23:09:59.564387 INFO::Found 0 missing values.
2024-10-16 23:09:59.568317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:59.56941 INFO::Done
2024-10-16 23:09:59.622464 INFO::Formatting Data.
2024-10-16 23:09:59.62389 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:59.625677 INFO::Removing potential empty rows and columns
2024-10-16 23:09:59.627511 INFO::Found 1 missing values.
2024-10-16 23:09:59.631024 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:59.632131 INFO::Done
2024-10-16 23:09:59.666956 INFO::Formatting Data.
2024-10-16 23:09:59.668383 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:59.669967 INFO::Removing potential empty rows and columns
2024-10-16 23:09:59.671546 INFO::Found 2 missing values.
2024-10-16 23:09:59.673106 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.
2024-10-16 23:09:59.67634 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:59.677438 INFO::Done
2024-10-16 23:09:59.696933 INFO::Formatting Data.
2024-10-16 23:09:59.698355 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:59.699919 INFO::Removing potential empty rows and columns
2024-10-16 23:09:59.701482 INFO::Found 2 missing values.
2024-10-16 23:09:59.703979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:59.70506 INFO::Done
2024-10-16 23:09:59.72467 INFO::Formatting Data.
2024-10-16 23:09:59.726092 INFO::Typecasting input to dataframe.
2024-10-16 23:09:59.727621 INFO::Replacing NaNs with NAs.
2024-10-16 23:09:59.729181 INFO::Removing potential empty rows and columns
2024-10-16 23:09:59.730833 INFO::Found 0 missing values.
2024-10-16 23:09:59.735228 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-16 23:09:59.736315 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
29.51 1.21 74.75
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.06 | 0.61 | 17.26 | |
| compute_asw | 0.05 | 0.00 | 0.05 | |
| count_existing | 0.01 | 0.00 | 0.01 | |
| generate_data_covariables | 0.03 | 0.00 | 0.03 | |
| generate_dataset | 0 | 0 | 0 | |