Yannis Schumann
| Snapshot Date: 2024-05-30 18:57:37 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-31 19:29:41 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 154/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | 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: 1.1.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.0.tar.gz |
| StartedAt: 2024-05-31 04:20:23 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 04:22:29 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 126.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 '1.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 8.11 0.52 17.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'BERT' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-05-31 04:21:21.842687 INFO::Formatting Data.
2024-05-31 04:21:21.845671 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:21.860982 INFO::Removing potential empty rows and columns
2024-05-31 04:21:22.128406 INFO::Found 0 missing values.
2024-05-31 04:21:22.131472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:22.132306 INFO::Done
2024-05-31 04:21:22.13305 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:22.146452 INFO::Starting hierarchical adjustment
2024-05-31 04:21:22.147501 INFO::Found 3 batches.
2024-05-31 04:21:22.148242 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:22.149556 INFO::Using default BPPARAM
2024-05-31 04:21:22.1503 INFO::Processing subtree level 1
2024-05-31 04:21:24.703358 INFO::Adjusting the last 1 batches sequentially
2024-05-31 04:21:24.70486 INFO::Done
2024-05-31 04:21:24.705633 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:24.707751 INFO::ASW Batch was -0.093187285543799 prior to batch effect correction and is now -0.093187285543799 .
2024-05-31 04:21:24.708812 INFO::Total function execution time is 2.86694002151489 s and adjustment time is 2.5575270652771 s ( 89.21 )
2024-05-31 04:21:24.725078 INFO::Formatting Data.
2024-05-31 04:21:24.726073 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:24.727161 INFO::Removing potential empty rows and columns
2024-05-31 04:21:24.728285 INFO::Found 0 missing values.
2024-05-31 04:21:24.729368 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 04:21:24.742489 INFO::Formatting Data.
2024-05-31 04:21:24.744111 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:24.745928 INFO::Removing potential empty rows and columns
2024-05-31 04:21:24.747908 INFO::Found 0 missing values.
2024-05-31 04:21:24.749693 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 04:21:24.777502 INFO::Formatting Data.
2024-05-31 04:21:24.779073 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:24.780584 INFO::Removing potential empty rows and columns
2024-05-31 04:21:24.781705 INFO::Found 0 missing values.
2024-05-31 04:21:24.782755 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 04:21:24.78632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:24.78704 INFO::Done
2024-05-31 04:21:24.787735 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:24.789751 INFO::Starting hierarchical adjustment
2024-05-31 04:21:24.790616 INFO::Found 2 batches.
2024-05-31 04:21:24.791402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:24.792196 INFO::Using default BPPARAM
2024-05-31 04:21:24.792909 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:24.793969 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:24.809677 INFO::Done
2024-05-31 04:21:24.81052 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:24.812563 INFO::ASW Batch was -0.0962931488022367 prior to batch effect correction and is now -0.124160028490946 .
2024-05-31 04:21:24.813524 INFO::Total function execution time is 0.0362129211425781 s and adjustment time is 0.0191709995269775 s ( 52.94 )
2024-05-31 04:21:24.816269 INFO::Formatting Data.
2024-05-31 04:21:24.817076 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:24.823851 INFO::Formatting Data.
2024-05-31 04:21:24.82472 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:24.825739 INFO::Removing potential empty rows and columns
2024-05-31 04:21:24.826839 INFO::Found 0 missing values.
2024-05-31 04:21:24.829367 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:24.830171 INFO::Done
2024-05-31 04:21:24.830977 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:24.833097 INFO::Starting hierarchical adjustment
2024-05-31 04:21:24.833977 INFO::Found 2 batches.
2024-05-31 04:21:24.834685 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:24.835452 INFO::Using default BPPARAM
2024-05-31 04:21:24.836146 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:24.837195 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:24.849309 INFO::Done
2024-05-31 04:21:24.850156 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:24.852226 INFO::ASW Batch was -0.0365546069490135 prior to batch effect correction and is now -0.122431956649118 .
2024-05-31 04:21:24.853193 INFO::Total function execution time is 0.0293741226196289 s and adjustment time is 0.0154449939727783 s ( 52.58 )
2024-05-31 04:21:24.854398 INFO::Formatting Data.
2024-05-31 04:21:24.855185 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:24.856184 INFO::Removing potential empty rows and columns
2024-05-31 04:21:24.85728 INFO::Found 0 missing values.
2024-05-31 04:21:24.859721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:24.860434 INFO::Done
2024-05-31 04:21:24.861133 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:24.863238 INFO::Starting hierarchical adjustment
2024-05-31 04:21:24.864115 INFO::Found 2 batches.
2024-05-31 04:21:24.864829 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:24.865594 INFO::Using default BPPARAM
2024-05-31 04:21:24.86629 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:24.867322 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:24.879178 INFO::Done
2024-05-31 04:21:24.880005 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:24.882076 INFO::ASW Batch was -0.0365546069490135 prior to batch effect correction and is now -0.122431956649118 .
2024-05-31 04:21:24.883036 INFO::Total function execution time is 0.0286450386047363 s and adjustment time is 0.0151841640472412 s ( 53.01 )
2024-05-31 04:21:26.541777 INFO::Formatting Data.
2024-05-31 04:21:26.542922 INFO::Recognized SummarizedExperiment
2024-05-31 04:21:26.544125 INFO::Typecasting input to dataframe.
2024-05-31 04:21:26.573821 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:26.575265 INFO::Removing potential empty rows and columns
2024-05-31 04:21:26.578303 INFO::Found 0 missing values.
2024-05-31 04:21:27.311517 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:27.312563 INFO::Done
2024-05-31 04:21:27.313377 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:27.317109 INFO::Starting hierarchical adjustment
2024-05-31 04:21:27.318039 INFO::Found 2 batches.
2024-05-31 04:21:27.318762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:27.320021 INFO::Using default BPPARAM
2024-05-31 04:21:27.32076 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:27.321953 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:27.363247 INFO::Done
2024-05-31 04:21:27.364167 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:27.367887 INFO::ASW Batch was -0.022136989619174 prior to batch effect correction and is now -0.0878278049148088 .
2024-05-31 04:21:27.368963 INFO::Total function execution time is 0.827587842941284 s and adjustment time is 0.045320987701416 s ( 5.48 )
2024-05-31 04:21:27.387608 INFO::Formatting Data.
2024-05-31 04:21:27.38858 INFO::Recognized SummarizedExperiment
2024-05-31 04:21:27.389322 INFO::Typecasting input to dataframe.
2024-05-31 04:21:27.397312 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:27.398621 INFO::Removing potential empty rows and columns
2024-05-31 04:21:27.401505 INFO::Found 0 missing values.
2024-05-31 04:21:27.4069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:27.407691 INFO::Done
2024-05-31 04:21:27.408422 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:27.412195 INFO::Starting hierarchical adjustment
2024-05-31 04:21:27.413083 INFO::Found 2 batches.
2024-05-31 04:21:27.413808 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:27.41459 INFO::Using default BPPARAM
2024-05-31 04:21:27.415294 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:27.416444 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:27.435207 INFO::Done
2024-05-31 04:21:27.436111 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:27.439985 INFO::ASW Batch was 0.0109677816717801 prior to batch effect correction and is now 0.0109677816717801 .
2024-05-31 04:21:27.441046 INFO::Total function execution time is 0.0534248352050781 s and adjustment time is 0.0222220420837402 s ( 41.59 )
2024-05-31 04:21:27.463458 INFO::Formatting Data.
2024-05-31 04:21:27.4645 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:27.465603 INFO::Removing potential empty rows and columns
2024-05-31 04:21:27.466761 INFO::Found 0 missing values.
2024-05-31 04:21:27.469464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:27.470207 INFO::Done
2024-05-31 04:21:27.470938 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:27.473061 INFO::Starting hierarchical adjustment
2024-05-31 04:21:27.473988 INFO::Found 3 batches.
2024-05-31 04:21:27.474701 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:27.475493 INFO::Using default BPPARAM
2024-05-31 04:21:27.476231 INFO::Processing subtree level 1
2024-05-31 04:21:36.530254 INFO::Adjusting the last 1 batches sequentially
2024-05-31 04:21:36.532533 INFO::Done
2024-05-31 04:21:36.533859 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:36.537018 INFO::ASW Batch was -0.124819556471683 prior to batch effect correction and is now -0.189040257471851 .
2024-05-31 04:21:36.538519 INFO::Total function execution time is 9.07508516311646 s and adjustment time is 9.05863308906555 s ( 99.82 )
2024-05-31 04:21:36.561856 INFO::Skipping initial DF formatting
2024-05-31 04:21:36.563276 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:36.569943 INFO::Starting hierarchical adjustment
2024-05-31 04:21:36.571418 INFO::Found 5 batches.
2024-05-31 04:21:36.572532 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:36.573677 INFO::Using default BPPARAM
2024-05-31 04:21:36.574733 INFO::Processing subtree level 1
2024-05-31 04:21:39.580795 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:39.583073 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:39.607353 INFO::Done
2024-05-31 04:21:39.608814 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:39.615649 INFO::ASW Batch was 0.471046841201186 prior to batch effect correction and is now 0.471046841201186 .
2024-05-31 04:21:39.617027 INFO::ASW Label was 0.415948937948204 prior to batch effect correction and is now 0.415948937948204 .
2024-05-31 04:21:39.618606 INFO::Total function execution time is 3.05686092376709 s and adjustment time is 3.03610396385193 s ( 99.32 )
2024-05-31 04:21:39.640621 INFO::Formatting Data.
2024-05-31 04:21:39.641597 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:39.642661 INFO::Removing potential empty rows and columns
2024-05-31 04:21:39.643784 INFO::Found 0 missing values.
2024-05-31 04:21:39.647267 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:39.64811 INFO::Done
2024-05-31 04:21:39.648829 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:39.65187 INFO::Starting hierarchical adjustment
2024-05-31 04:21:39.653076 INFO::Found 5 batches.
2024-05-31 04:21:39.654258 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:39.655569 INFO::Using default BPPARAM
2024-05-31 04:21:39.6568 INFO::Processing subtree level 1
2024-05-31 04:21:42.727291 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:42.729032 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:42.741626 INFO::Done
2024-05-31 04:21:42.742548 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:42.745788 INFO::ASW Batch was 0.253332109949731 prior to batch effect correction and is now -0.0157015893676379 .
2024-05-31 04:21:42.746606 INFO::ASW Label was 0.510723528637291 prior to batch effect correction and is now 0.820893394388687 .
2024-05-31 04:21:42.747565 INFO::Total function execution time is 3.10704398155212 s and adjustment time is 3.08877205848694 s ( 99.41 )
2024-05-31 04:21:42.748692 INFO::Formatting Data.
2024-05-31 04:21:42.7495 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:42.750534 INFO::Removing potential empty rows and columns
2024-05-31 04:21:42.751635 INFO::Found 0 missing values.
2024-05-31 04:21:42.755351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:42.756089 INFO::Done
2024-05-31 04:21:42.756787 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:42.759781 INFO::Starting hierarchical adjustment
2024-05-31 04:21:42.76066 INFO::Found 5 batches.
2024-05-31 04:21:42.761369 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:42.762148 INFO::Using default BPPARAM
2024-05-31 04:21:42.762844 INFO::Processing subtree level 1
2024-05-31 04:21:45.739977 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:45.742068 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:45.759069 INFO::Done
2024-05-31 04:21:45.760396 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:45.764951 INFO::ASW Batch was 0.253332109949731 prior to batch effect correction and is now -0.0157015893676379 .
2024-05-31 04:21:45.765804 INFO::ASW Label was 0.510723528637291 prior to batch effect correction and is now 0.820893394388687 .
2024-05-31 04:21:45.766787 INFO::Total function execution time is 3.01810002326965 s and adjustment time is 2.9984610080719 s ( 99.35 )
2024-05-31 04:21:45.789222 INFO::Formatting Data.
2024-05-31 04:21:45.7911 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:45.793061 INFO::Removing potential empty rows and columns
2024-05-31 04:21:45.79501 INFO::Found 0 missing values.
2024-05-31 04:21:45.800932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:45.80226 INFO::Done
2024-05-31 04:21:45.803533 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:45.808574 INFO::Starting hierarchical adjustment
2024-05-31 04:21:45.810137 INFO::Found 5 batches.
2024-05-31 04:21:45.811418 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:45.812598 INFO::Using default BPPARAM
2024-05-31 04:21:45.813663 INFO::Processing subtree level 1
2024-05-31 04:21:48.85218 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:48.854229 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:48.871047 INFO::Done
2024-05-31 04:21:48.872334 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:48.876551 INFO::ASW Batch was 0.293552337528353 prior to batch effect correction and is now -0.0854554573356911 .
2024-05-31 04:21:48.877763 INFO::ASW Label was 0.277523864716941 prior to batch effect correction and is now 0.893809462089955 .
2024-05-31 04:21:48.878785 INFO::Total function execution time is 3.0898060798645 s and adjustment time is 3.06111884117126 s ( 99.07 )
2024-05-31 04:21:48.879737 INFO::Formatting Data.
2024-05-31 04:21:48.880523 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:48.881544 INFO::Removing potential empty rows and columns
2024-05-31 04:21:48.882608 INFO::Found 0 missing values.
2024-05-31 04:21:48.886035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:48.886762 INFO::Done
2024-05-31 04:21:48.887453 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:48.890494 INFO::Starting hierarchical adjustment
2024-05-31 04:21:48.891382 INFO::Found 5 batches.
2024-05-31 04:21:48.892083 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:48.892898 INFO::Using default BPPARAM
2024-05-31 04:21:48.893625 INFO::Processing subtree level 1
2024-05-31 04:21:51.892244 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:51.894176 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:51.912205 INFO::Done
2024-05-31 04:21:51.913558 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:51.918078 INFO::ASW Batch was 0.293552337528353 prior to batch effect correction and is now -0.0854554573356911 .
2024-05-31 04:21:51.919347 INFO::ASW Label was 0.277523864716941 prior to batch effect correction and is now 0.893809462089955 .
2024-05-31 04:21:51.920873 INFO::Total function execution time is 3.04106211662292 s and adjustment time is 3.02089285850525 s ( 99.34 )
2024-05-31 04:21:51.945098 INFO::Formatting Data.
2024-05-31 04:21:51.946634 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:51.948334 INFO::Removing potential empty rows and columns
2024-05-31 04:21:51.95015 INFO::Found 0 missing values.
2024-05-31 04:21:51.954278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:51.955498 INFO::Done
2024-05-31 04:21:51.956717 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:51.961429 INFO::Starting hierarchical adjustment
2024-05-31 04:21:51.962858 INFO::Found 2 batches.
2024-05-31 04:21:51.964071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:51.965376 INFO::Using default BPPARAM
2024-05-31 04:21:51.966581 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:51.968341 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:51.987863 INFO::Done
2024-05-31 04:21:51.989292 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:51.99405 INFO::ASW Batch was 0.458230638221374 prior to batch effect correction and is now -0.0376991880116593 .
2024-05-31 04:21:51.995347 INFO::ASW Label was 0.63971437767027 prior to batch effect correction and is now 0.957069018987929 .
2024-05-31 04:21:51.9969 INFO::Total function execution time is 0.0519099235534668 s and adjustment time is 0.0251710414886475 s ( 48.49 )
2024-05-31 04:21:51.998442 INFO::Formatting Data.
2024-05-31 04:21:51.999741 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:52.001393 INFO::Removing potential empty rows and columns
2024-05-31 04:21:52.00318 INFO::Found 0 missing values.
2024-05-31 04:21:52.00721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:52.008399 INFO::Done
2024-05-31 04:21:52.00954 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:52.014207 INFO::Starting hierarchical adjustment
2024-05-31 04:21:52.015671 INFO::Found 2 batches.
2024-05-31 04:21:52.016898 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:52.018222 INFO::Using default BPPARAM
2024-05-31 04:21:52.019438 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:52.021205 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:52.041254 INFO::Done
2024-05-31 04:21:52.042617 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:52.045652 INFO::ASW Batch was 0.458230638221374 prior to batch effect correction and is now -0.0376991880116593 .
2024-05-31 04:21:52.046425 INFO::ASW Label was 0.63971437767027 prior to batch effect correction and is now 0.957069018987929 .
2024-05-31 04:21:52.047371 INFO::Total function execution time is 0.04901123046875 s and adjustment time is 0.0257620811462402 s ( 52.56 )
2024-05-31 04:21:52.06581 INFO::Formatting Data.
2024-05-31 04:21:52.067329 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:52.068995 INFO::Removing potential empty rows and columns
2024-05-31 04:21:52.07069 INFO::Found 0 missing values.
2024-05-31 04:21:52.07414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:52.075342 INFO::Done
2024-05-31 04:21:52.076569 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:52.079656 INFO::Starting hierarchical adjustment
2024-05-31 04:21:52.081034 INFO::Found 2 batches.
2024-05-31 04:21:52.082201 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:52.083502 INFO::Using default BPPARAM
2024-05-31 04:21:52.084691 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:52.086409 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:52.119084 INFO::Done
2024-05-31 04:21:52.119949 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:52.121939 INFO::ASW Batch was -0.159803960033538 prior to batch effect correction and is now -0.16533695878185 .
2024-05-31 04:21:52.122927 INFO::Total function execution time is 0.0573091506958008 s and adjustment time is 0.038261890411377 s ( 66.76 )
2024-05-31 04:21:52.138549 INFO::Formatting Data.
2024-05-31 04:21:52.139539 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:52.140626 INFO::Removing potential empty rows and columns
2024-05-31 04:21:52.141757 INFO::Found 0 missing values.
2024-05-31 04:21:52.143001 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 04:21:52.146882 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:52.147625 INFO::Done
2024-05-31 04:21:52.148327 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:52.151273 INFO::Starting hierarchical adjustment
2024-05-31 04:21:52.152169 INFO::Found 2 batches.
2024-05-31 04:21:52.152882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:52.153661 INFO::Using default BPPARAM
2024-05-31 04:21:52.154415 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:52.15571 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:52.183201 INFO::Done
2024-05-31 04:21:52.184715 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:52.190415 INFO::ASW Batch was 0.453946396224972 prior to batch effect correction and is now 0.0368017079472313 .
2024-05-31 04:21:52.191928 INFO::ASW Label was 0.646095834235171 prior to batch effect correction and is now 0.922334554742619 .
2024-05-31 04:21:52.193757 INFO::Total function execution time is 0.0551300048828125 s and adjustment time is 0.0310330390930176 s ( 56.29 )
2024-05-31 04:21:52.195577 INFO::Formatting Data.
2024-05-31 04:21:52.197059 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:52.199025 INFO::Removing potential empty rows and columns
2024-05-31 04:21:52.201033 INFO::Found 0 missing values.
2024-05-31 04:21:52.202663 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 04:21:52.209108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:52.210332 INFO::Done
2024-05-31 04:21:52.211544 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:52.21625 INFO::Starting hierarchical adjustment
2024-05-31 04:21:52.217724 INFO::Found 2 batches.
2024-05-31 04:21:52.218951 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:52.220272 INFO::Using default BPPARAM
2024-05-31 04:21:52.221468 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:21:52.223277 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:21:52.245494 INFO::Done
2024-05-31 04:21:52.246899 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:52.251685 INFO::ASW Batch was 0.453946396224972 prior to batch effect correction and is now 0.0368017079472313 .
2024-05-31 04:21:52.252979 INFO::ASW Label was 0.646095834235171 prior to batch effect correction and is now 0.922334554742619 .
2024-05-31 04:21:52.254568 INFO::Total function execution time is 0.0590970516204834 s and adjustment time is 0.027940034866333 s ( 47.28 )
2024-05-31 04:21:52.491427 INFO::Formatting Data.
2024-05-31 04:21:52.492509 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:52.493689 INFO::Removing potential empty rows and columns
2024-05-31 04:21:52.494929 INFO::Found 0 missing values.
2024-05-31 04:21:52.4981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:52.498925 INFO::Done
2024-05-31 04:21:52.49974 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:52.502143 INFO::Starting hierarchical adjustment
2024-05-31 04:21:52.503123 INFO::Found 3 batches.
2024-05-31 04:21:52.503897 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:52.504772 INFO::Using default BPPARAM
2024-05-31 04:21:52.505561 INFO::Processing subtree level 1
2024-05-31 04:21:55.119797 INFO::Adjusting the last 1 batches sequentially
2024-05-31 04:21:55.122146 INFO::Done
2024-05-31 04:21:55.123564 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:55.127033 INFO::ASW Batch was -0.113797559885922 prior to batch effect correction and is now -0.113797559885922 .
2024-05-31 04:21:55.128795 INFO::Total function execution time is 2.63738298416138 s and adjustment time is 2.61910581588745 s ( 99.31 )
2024-05-31 04:21:55.130707 INFO::Formatting Data.
2024-05-31 04:21:55.132147 INFO::Typecasting input to dataframe.
2024-05-31 04:21:55.133732 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:55.135483 INFO::Removing potential empty rows and columns
2024-05-31 04:21:55.137429 INFO::Found 0 missing values.
2024-05-31 04:21:55.142128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:55.143428 INFO::Done
2024-05-31 04:21:55.144704 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:55.148103 INFO::Starting hierarchical adjustment
2024-05-31 04:21:55.149599 INFO::Found 3 batches.
2024-05-31 04:21:55.150846 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:55.152192 INFO::Using default BPPARAM
2024-05-31 04:21:55.153427 INFO::Processing subtree level 1
2024-05-31 04:21:58.025131 INFO::Adjusting the last 1 batches sequentially
2024-05-31 04:21:58.027527 INFO::Done
2024-05-31 04:21:58.028932 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:21:58.032299 INFO::ASW Batch was -0.113797559885922 prior to batch effect correction and is now -0.113797559885922 .
2024-05-31 04:21:58.033988 INFO::Total function execution time is 2.90332698822021 s and adjustment time is 2.87811899185181 s ( 99.13 )
2024-05-31 04:21:58.058458 INFO::Formatting Data.
2024-05-31 04:21:58.060104 INFO::Typecasting input to dataframe.
2024-05-31 04:21:58.061762 INFO::Replacing NaNs with NAs.
2024-05-31 04:21:58.063474 INFO::Removing potential empty rows and columns
2024-05-31 04:21:58.065418 INFO::Found 0 missing values.
2024-05-31 04:21:58.070013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:21:58.071334 INFO::Done
2024-05-31 04:21:58.072632 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:21:58.075833 INFO::Starting hierarchical adjustment
2024-05-31 04:21:58.076883 INFO::Found 3 batches.
2024-05-31 04:21:58.077603 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:21:58.078374 INFO::Using default BPPARAM
2024-05-31 04:21:58.079081 INFO::Processing subtree level 1
2024-05-31 04:22:00.757309 INFO::Adjusting the last 1 batches sequentially
2024-05-31 04:22:00.759575 INFO::Done
2024-05-31 04:22:00.760839 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:22:00.763899 INFO::ASW Batch was -0.00814525259933345 prior to batch effect correction and is now -0.00814525259933345 .
2024-05-31 04:22:00.765409 INFO::Total function execution time is 2.70708680152893 s and adjustment time is 2.68278503417969 s ( 99.1 )
2024-05-31 04:22:03.465353 INFO::Formatting Data.
2024-05-31 04:22:03.466411 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:03.467643 INFO::Removing potential empty rows and columns
2024-05-31 04:22:03.469897 INFO::Found 1000 missing values.
2024-05-31 04:22:03.483362 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:03.484223 INFO::Done
2024-05-31 04:22:03.484957 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:22:03.491014 INFO::Starting hierarchical adjustment
2024-05-31 04:22:03.491934 INFO::Found 10 batches.
2024-05-31 04:22:03.492649 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:22:03.493422 INFO::Using default BPPARAM
2024-05-31 04:22:03.494129 INFO::Processing subtree level 1
2024-05-31 04:22:06.516153 INFO::Processing subtree level 2
2024-05-31 04:22:09.694824 INFO::Adjusting the last 1 batches sequentially
2024-05-31 04:22:09.697356 INFO::Done
2024-05-31 04:22:09.698879 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:22:09.709264 INFO::ASW Batch was 0.532166166861055 prior to batch effect correction and is now 0.532166166861055 .
2024-05-31 04:22:09.710891 INFO::ASW Label was 0.310424040458427 prior to batch effect correction and is now 0.310424040458427 .
2024-05-31 04:22:09.712851 INFO::Total function execution time is 6.24745416641235 s and adjustment time is 6.2054660320282 s ( 99.33 )
2024-05-31 04:22:09.714637 INFO::Formatting Data.
2024-05-31 04:22:09.716144 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:09.718317 INFO::Removing potential empty rows and columns
2024-05-31 04:22:09.722205 INFO::Found 1000 missing values.
2024-05-31 04:22:09.744903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:09.745905 INFO::Done
2024-05-31 04:22:09.746691 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:22:09.753095 INFO::Starting hierarchical adjustment
2024-05-31 04:22:09.754143 INFO::Found 10 batches.
2024-05-31 04:22:10.504321 INFO::Set up parallel execution backend with 2 workers
2024-05-31 04:22:10.505862 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-31 04:22:13.575335 INFO::Adjusting the last 2 batches sequentially
2024-05-31 04:22:13.577703 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 04:22:13.603669 INFO::Done
2024-05-31 04:22:13.605172 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:22:13.61487 INFO::ASW Batch was 0.532166166861055 prior to batch effect correction and is now 0.532166166861055 .
2024-05-31 04:22:13.616376 INFO::ASW Label was 0.310424040458427 prior to batch effect correction and is now 0.310424040458427 .
2024-05-31 04:22:13.618053 INFO::Total function execution time is 3.9034628868103 s and adjustment time is 3.84958791732788 s ( 98.62 )
2024-05-31 04:22:16.521996 INFO::Formatting Data.
2024-05-31 04:22:16.523036 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:16.524165 INFO::Removing potential empty rows and columns
2024-05-31 04:22:16.525336 INFO::Found 0 missing values.
2024-05-31 04:22:16.528836 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:16.529596 INFO::Done
2024-05-31 04:22:16.530302 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 04:22:16.533046 INFO::Starting hierarchical adjustment
2024-05-31 04:22:16.533938 INFO::Found 3 batches.
2024-05-31 04:22:16.534659 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 04:22:16.535437 INFO::Using default BPPARAM
2024-05-31 04:22:16.536144 INFO::Processing subtree level 1
2024-05-31 04:22:19.519631 INFO::Adjusting the last 1 batches sequentially
2024-05-31 04:22:19.52186 INFO::Done
2024-05-31 04:22:19.523104 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 04:22:19.527068 INFO::ASW Batch was 0.24671783340004 prior to batch effect correction and is now -0.1726038596106 .
2024-05-31 04:22:19.528276 INFO::ASW Label was -0.187725226221699 prior to batch effect correction and is now -0.0460982058427269 .
2024-05-31 04:22:19.529714 INFO::Total function execution time is 3.00778007507324 s and adjustment time is 2.98800206184387 s ( 99.34 )
2024-05-31 04:22:19.71252 INFO::Formatting Data.
2024-05-31 04:22:19.71352 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:19.714619 INFO::Removing potential empty rows and columns
2024-05-31 04:22:19.715735 INFO::Found 2 missing values.
2024-05-31 04:22:19.718238 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:19.718959 INFO::Done
2024-05-31 04:22:19.758829 INFO::Found NA in Reference column
2024-05-31 04:22:19.776323 INFO::Require at least two references per batch.
2024-05-31 04:22:19.807255 INFO::Formatting Data.
2024-05-31 04:22:19.808222 INFO::Recognized SummarizedExperiment
2024-05-31 04:22:19.808984 INFO::Typecasting input to dataframe.
2024-05-31 04:22:19.816512 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:19.817764 INFO::Removing potential empty rows and columns
2024-05-31 04:22:19.820385 INFO::Found 0 missing values.
2024-05-31 04:22:19.825332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:19.826082 INFO::Done
2024-05-31 04:22:19.839999 INFO::Formatting Data.
2024-05-31 04:22:19.840937 INFO::Recognized SummarizedExperiment
2024-05-31 04:22:19.841659 INFO::Typecasting input to dataframe.
2024-05-31 04:22:19.856156 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:19.857555 INFO::Removing potential empty rows and columns
2024-05-31 04:22:19.860382 INFO::Found 0 missing values.
2024-05-31 04:22:19.868203 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:19.869038 INFO::Done
2024-05-31 04:22:19.883499 INFO::Formatting Data.
2024-05-31 04:22:19.884437 INFO::Recognized SummarizedExperiment
2024-05-31 04:22:19.885187 INFO::Typecasting input to dataframe.
2024-05-31 04:22:19.898927 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:19.900088 INFO::Removing potential empty rows and columns
2024-05-31 04:22:19.901275 INFO::Found 0 missing values.
2024-05-31 04:22:19.902394 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 04:22:19.906048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:19.906768 INFO::Done
2024-05-31 04:22:19.920935 INFO::Formatting Data.
2024-05-31 04:22:19.921931 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:19.922961 INFO::Removing potential empty rows and columns
2024-05-31 04:22:19.924072 INFO::Found 0 missing values.
2024-05-31 04:22:19.926665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:19.927385 INFO::Done
2024-05-31 04:22:19.942524 INFO::Formatting Data.
2024-05-31 04:22:19.943486 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:19.944521 INFO::Removing potential empty rows and columns
2024-05-31 04:22:19.945659 INFO::Found 0 missing values.
2024-05-31 04:22:19.948314 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:19.949044 INFO::Done
2024-05-31 04:22:19.988521 INFO::Formatting Data.
2024-05-31 04:22:19.989522 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:19.990693 INFO::Removing potential empty rows and columns
2024-05-31 04:22:19.991914 INFO::Found 1 missing values.
2024-05-31 04:22:19.994237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:19.994966 INFO::Done
2024-05-31 04:22:20.019803 INFO::Formatting Data.
2024-05-31 04:22:20.020895 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:20.022006 INFO::Removing potential empty rows and columns
2024-05-31 04:22:20.023073 INFO::Found 2 missing values.
2024-05-31 04:22:20.024345 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 04:22:20.026929 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:20.028063 INFO::Done
2024-05-31 04:22:20.042232 INFO::Formatting Data.
2024-05-31 04:22:20.043231 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:20.044868 INFO::Removing potential empty rows and columns
2024-05-31 04:22:20.046614 INFO::Found 2 missing values.
2024-05-31 04:22:20.048347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:20.049064 INFO::Done
2024-05-31 04:22:20.065844 INFO::Formatting Data.
2024-05-31 04:22:20.067098 INFO::Typecasting input to dataframe.
2024-05-31 04:22:20.068128 INFO::Replacing NaNs with NAs.
2024-05-31 04:22:20.06917 INFO::Removing potential empty rows and columns
2024-05-31 04:22:20.070422 INFO::Found 0 missing values.
2024-05-31 04:22:20.073285 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 04:22:20.074012 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
27.53 1.43 71.79
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.11 | 0.52 | 17.16 | |
| compute_asw | 0.03 | 0.00 | 0.03 | |
| count_existing | 0.01 | 0.00 | 0.02 | |
| generate_data_covariables | 0.02 | 0.00 | 0.01 | |
| generate_dataset | 0.01 | 0.00 | 0.02 | |