Yannis Schumann
| Snapshot Date: 2024-05-20 14:05:07 -0400 (Mon, 20 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 2024-05-22 11:36:36 -0400 (Wed, 22 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" | 4665 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
| 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 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.0 |
| Command: 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: 2024-05-20 22:27:49 -0400 (Mon, 20 May 2024) |
| EndedAt: 2024-05-20 22:29:52 -0400 (Mon, 20 May 2024) |
| EllapsedTime: 122.8 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 7.42 0.39 15.59
* 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")
2024-05-20 22:28:46.147131 INFO::Formatting Data.
2024-05-20 22:28:46.149339 INFO::Replacing NaNs with NAs.
2024-05-20 22:28:46.158378 INFO::Removing potential empty rows and columns
2024-05-20 22:28:46.369359 INFO::Found 0 missing values.
2024-05-20 22:28:46.372845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:28:46.3737 INFO::Done
2024-05-20 22:28:46.374443 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:28:46.390306 INFO::Starting hierarchical adjustment
2024-05-20 22:28:46.391364 INFO::Found 3 batches.
2024-05-20 22:28:46.392127 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:28:46.39341 INFO::Using default BPPARAM
2024-05-20 22:28:46.394146 INFO::Processing subtree level 1
2024-05-20 22:28:49.273605 INFO::Adjusting the last 1 batches sequentially
2024-05-20 22:28:49.27592 INFO::Done
2024-05-20 22:28:49.277309 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:28:49.280748 INFO::ASW Batch was -0.0113686417507312 prior to batch effect correction and is now -0.0113686417507312 .
2024-05-20 22:28:49.282462 INFO::Total function execution time is 3.13567090034485 s and adjustment time is 2.88467812538147 s ( 92 )
2024-05-20 22:28:49.307586 INFO::Formatting Data.
2024-05-20 22:28:49.309334 INFO::Replacing NaNs with NAs.
2024-05-20 22:28:49.311344 INFO::Removing potential empty rows and columns
2024-05-20 22:28:49.313549 INFO::Found 0 missing values.
2024-05-20 22:28:49.315477 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.
2024-05-20 22:28:49.328477 INFO::Formatting Data.
2024-05-20 22:28:49.329894 INFO::Replacing NaNs with NAs.
2024-05-20 22:28:49.331444 INFO::Removing potential empty rows and columns
2024-05-20 22:28:49.333181 INFO::Found 0 missing values.
2024-05-20 22:28:49.334876 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.
2024-05-20 22:28:49.361228 INFO::Formatting Data.
2024-05-20 22:28:49.362747 INFO::Replacing NaNs with NAs.
2024-05-20 22:28:49.364417 INFO::Removing potential empty rows and columns
2024-05-20 22:28:49.366138 INFO::Found 0 missing values.
2024-05-20 22:28:49.367743 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.
2024-05-20 22:28:49.373436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:28:49.3746 INFO::Done
2024-05-20 22:28:49.375791 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:28:49.378903 INFO::Starting hierarchical adjustment
2024-05-20 22:28:49.380287 INFO::Found 2 batches.
2024-05-20 22:28:49.381547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:28:49.38282 INFO::Using default BPPARAM
2024-05-20 22:28:49.383989 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:28:49.385725 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:28:49.410165 INFO::Done
2024-05-20 22:28:49.411047 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:28:49.414535 INFO::ASW Batch was 0.00877528854724267 prior to batch effect correction and is now -0.0993270152745463 .
2024-05-20 22:28:49.415615 INFO::Total function execution time is 0.0545608997344971 s and adjustment time is 0.0300638675689697 s ( 55.1 )
2024-05-20 22:28:49.418626 INFO::Formatting Data.
2024-05-20 22:28:49.419435 INFO::Replacing NaNs with NAs.
2024-05-20 22:28:49.426514 INFO::Formatting Data.
2024-05-20 22:28:49.427357 INFO::Replacing NaNs with NAs.
2024-05-20 22:28:49.428359 INFO::Removing potential empty rows and columns
2024-05-20 22:28:49.429447 INFO::Found 0 missing values.
2024-05-20 22:28:49.431856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:28:49.432565 INFO::Done
2024-05-20 22:28:49.43325 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:28:49.435285 INFO::Starting hierarchical adjustment
2024-05-20 22:28:49.436145 INFO::Found 2 batches.
2024-05-20 22:28:49.436866 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:28:49.43763 INFO::Using default BPPARAM
2024-05-20 22:28:49.438352 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:28:49.439406 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:28:49.451294 INFO::Done
2024-05-20 22:28:49.452144 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:28:49.454247 INFO::ASW Batch was 0.0117292901949996 prior to batch effect correction and is now -0.114752212421189 .
2024-05-20 22:28:49.455211 INFO::Total function execution time is 0.0287139415740967 s and adjustment time is 0.0152599811553955 s ( 53.14 )
2024-05-20 22:28:49.456416 INFO::Formatting Data.
2024-05-20 22:28:49.457216 INFO::Replacing NaNs with NAs.
2024-05-20 22:28:49.458231 INFO::Removing potential empty rows and columns
2024-05-20 22:28:49.459333 INFO::Found 0 missing values.
2024-05-20 22:28:49.46182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:28:49.462542 INFO::Done
2024-05-20 22:28:49.463253 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:28:49.465365 INFO::Starting hierarchical adjustment
2024-05-20 22:28:49.466242 INFO::Found 2 batches.
2024-05-20 22:28:49.466966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:28:49.467736 INFO::Using default BPPARAM
2024-05-20 22:28:49.46843 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:28:49.469489 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:28:49.481369 INFO::Done
2024-05-20 22:28:49.482185 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:28:49.484213 INFO::ASW Batch was 0.0117292901949996 prior to batch effect correction and is now -0.114752212421189 .
2024-05-20 22:28:49.48516 INFO::Total function execution time is 0.0287420749664307 s and adjustment time is 0.0152530670166016 s ( 53.07 )
2024-05-20 22:28:51.982862 INFO::Formatting Data.
2024-05-20 22:28:51.983796 INFO::Recognized SummarizedExperiment
2024-05-20 22:28:51.984528 INFO::Typecasting input to dataframe.
2024-05-20 22:28:52.012653 INFO::Replacing NaNs with NAs.
2024-05-20 22:28:52.014066 INFO::Removing potential empty rows and columns
2024-05-20 22:28:52.017084 INFO::Found 0 missing values.
2024-05-20 22:28:52.022761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:28:52.023633 INFO::Done
2024-05-20 22:28:52.024408 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:28:52.028234 INFO::Starting hierarchical adjustment
2024-05-20 22:28:52.02914 INFO::Found 2 batches.
2024-05-20 22:28:52.02985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:28:52.031125 INFO::Using default BPPARAM
2024-05-20 22:28:52.031875 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:28:52.033096 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:28:52.078522 INFO::Done
2024-05-20 22:28:52.079445 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:28:52.083358 INFO::ASW Batch was 0.0242743443491148 prior to batch effect correction and is now -0.0893589079735362 .
2024-05-20 22:28:52.084425 INFO::Total function execution time is 0.101850032806396 s and adjustment time is 0.0494930744171143 s ( 48.59 )
2024-05-20 22:28:52.103416 INFO::Formatting Data.
2024-05-20 22:28:52.104376 INFO::Recognized SummarizedExperiment
2024-05-20 22:28:52.105136 INFO::Typecasting input to dataframe.
2024-05-20 22:28:52.113279 INFO::Replacing NaNs with NAs.
2024-05-20 22:28:52.114626 INFO::Removing potential empty rows and columns
2024-05-20 22:28:52.117561 INFO::Found 0 missing values.
2024-05-20 22:28:52.123101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:28:52.123864 INFO::Done
2024-05-20 22:28:52.12458 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:28:52.128339 INFO::Starting hierarchical adjustment
2024-05-20 22:28:52.12924 INFO::Found 2 batches.
2024-05-20 22:28:52.12995 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:28:52.13079 INFO::Using default BPPARAM
2024-05-20 22:28:52.131507 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:28:52.132679 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:28:52.157839 INFO::Done
2024-05-20 22:28:52.159399 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:28:52.164411 INFO::ASW Batch was 0.000971946068921624 prior to batch effect correction and is now 0.000971946068921624 .
2024-05-20 22:28:52.165545 INFO::Total function execution time is 0.0620968341827393 s and adjustment time is 0.0286290645599365 s ( 46.1 )
2024-05-20 22:28:52.187032 INFO::Formatting Data.
2024-05-20 22:28:52.188014 INFO::Replacing NaNs with NAs.
2024-05-20 22:28:52.189093 INFO::Removing potential empty rows and columns
2024-05-20 22:28:52.190243 INFO::Found 0 missing values.
2024-05-20 22:28:52.193614 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:28:52.194365 INFO::Done
2024-05-20 22:28:52.195107 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:28:52.197376 INFO::Starting hierarchical adjustment
2024-05-20 22:28:52.198327 INFO::Found 3 batches.
2024-05-20 22:28:52.199115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:28:52.199975 INFO::Using default BPPARAM
2024-05-20 22:28:52.200793 INFO::Processing subtree level 1
2024-05-20 22:29:01.413308 INFO::Adjusting the last 1 batches sequentially
2024-05-20 22:29:01.415644 INFO::Done
2024-05-20 22:29:01.417129 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:01.420466 INFO::ASW Batch was -0.0204113858689886 prior to batch effect correction and is now -0.159126917266593 .
2024-05-20 22:29:01.421995 INFO::Total function execution time is 9.23495817184448 s and adjustment time is 9.21738910675049 s ( 99.81 )
2024-05-20 22:29:01.446008 INFO::Skipping initial DF formatting
2024-05-20 22:29:01.447258 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:01.451636 INFO::Starting hierarchical adjustment
2024-05-20 22:29:01.452585 INFO::Found 5 batches.
2024-05-20 22:29:01.453311 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:01.454094 INFO::Using default BPPARAM
2024-05-20 22:29:01.454802 INFO::Processing subtree level 1
2024-05-20 22:29:04.272978 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:04.274421 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:04.288425 INFO::Done
2024-05-20 22:29:04.289273 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:04.293368 INFO::ASW Batch was 0.511154901697755 prior to batch effect correction and is now 0.511154901697755 .
2024-05-20 22:29:04.294142 INFO::ASW Label was 0.350639200678424 prior to batch effect correction and is now 0.350639200678424 .
2024-05-20 22:29:04.295095 INFO::Total function execution time is 2.84928393363953 s and adjustment time is 2.83598494529724 s ( 99.53 )
2024-05-20 22:29:04.322306 INFO::Formatting Data.
2024-05-20 22:29:04.323852 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:04.325577 INFO::Removing potential empty rows and columns
2024-05-20 22:29:04.327332 INFO::Found 0 missing values.
2024-05-20 22:29:04.333145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:04.334379 INFO::Done
2024-05-20 22:29:04.335592 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:04.340373 INFO::Starting hierarchical adjustment
2024-05-20 22:29:04.341829 INFO::Found 5 batches.
2024-05-20 22:29:04.343028 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:04.344334 INFO::Using default BPPARAM
2024-05-20 22:29:04.345516 INFO::Processing subtree level 1
2024-05-20 22:29:07.176442 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:07.178493 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:07.19577 INFO::Done
2024-05-20 22:29:07.197076 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:07.201432 INFO::ASW Batch was 0.50836456557918 prior to batch effect correction and is now -0.00839995450275309 .
2024-05-20 22:29:07.202268 INFO::ASW Label was 0.117914287140488 prior to batch effect correction and is now 0.70659714270822 .
2024-05-20 22:29:07.203222 INFO::Total function execution time is 2.88109803199768 s and adjustment time is 2.8541271686554 s ( 99.06 )
2024-05-20 22:29:07.204168 INFO::Formatting Data.
2024-05-20 22:29:07.204958 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:07.205989 INFO::Removing potential empty rows and columns
2024-05-20 22:29:07.207089 INFO::Found 0 missing values.
2024-05-20 22:29:07.210514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:07.211276 INFO::Done
2024-05-20 22:29:07.212008 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:07.215072 INFO::Starting hierarchical adjustment
2024-05-20 22:29:07.216026 INFO::Found 5 batches.
2024-05-20 22:29:07.216749 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:07.217526 INFO::Using default BPPARAM
2024-05-20 22:29:07.218226 INFO::Processing subtree level 1
2024-05-20 22:29:10.239953 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:10.241872 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:10.259928 INFO::Done
2024-05-20 22:29:10.261212 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:10.265641 INFO::ASW Batch was 0.50836456557918 prior to batch effect correction and is now -0.00839995450275309 .
2024-05-20 22:29:10.266791 INFO::ASW Label was 0.117914287140488 prior to batch effect correction and is now 0.70659714270822 .
2024-05-20 22:29:10.268182 INFO::Total function execution time is 3.06395196914673 s and adjustment time is 3.04396104812622 s ( 99.35 )
2024-05-20 22:29:10.292233 INFO::Formatting Data.
2024-05-20 22:29:10.293912 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:10.296083 INFO::Removing potential empty rows and columns
2024-05-20 22:29:10.297875 INFO::Found 0 missing values.
2024-05-20 22:29:10.303199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:10.304153 INFO::Done
2024-05-20 22:29:10.30505 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:10.308243 INFO::Starting hierarchical adjustment
2024-05-20 22:29:10.309128 INFO::Found 5 batches.
2024-05-20 22:29:10.310518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:10.311333 INFO::Using default BPPARAM
2024-05-20 22:29:10.312052 INFO::Processing subtree level 1
2024-05-20 22:29:13.39714 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:13.399373 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:13.417324 INFO::Done
2024-05-20 22:29:13.418732 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:13.423392 INFO::ASW Batch was 0.394109590414116 prior to batch effect correction and is now 0.0140357306078544 .
2024-05-20 22:29:13.4247 INFO::ASW Label was 0.223443562756055 prior to batch effect correction and is now 0.717517631038127 .
2024-05-20 22:29:13.426202 INFO::Total function execution time is 3.13407397270203 s and adjustment time is 3.10824990272522 s ( 99.18 )
2024-05-20 22:29:13.427705 INFO::Formatting Data.
2024-05-20 22:29:13.428962 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:13.430602 INFO::Removing potential empty rows and columns
2024-05-20 22:29:13.432222 INFO::Found 0 missing values.
2024-05-20 22:29:13.437313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:13.439731 INFO::Done
2024-05-20 22:29:13.440895 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:13.445331 INFO::Starting hierarchical adjustment
2024-05-20 22:29:13.446245 INFO::Found 5 batches.
2024-05-20 22:29:13.446954 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:13.447724 INFO::Using default BPPARAM
2024-05-20 22:29:13.448422 INFO::Processing subtree level 1
2024-05-20 22:29:16.348723 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:16.350759 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:16.369212 INFO::Done
2024-05-20 22:29:16.370646 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:16.375506 INFO::ASW Batch was 0.394109590414116 prior to batch effect correction and is now 0.0140357306078544 .
2024-05-20 22:29:16.376742 INFO::ASW Label was 0.223443562756055 prior to batch effect correction and is now 0.717517631038127 .
2024-05-20 22:29:16.378274 INFO::Total function execution time is 2.9505820274353 s and adjustment time is 2.9230260848999 s ( 99.07 )
2024-05-20 22:29:16.402137 INFO::Formatting Data.
2024-05-20 22:29:16.403572 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:16.405181 INFO::Removing potential empty rows and columns
2024-05-20 22:29:16.406836 INFO::Found 0 missing values.
2024-05-20 22:29:16.410615 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:16.411729 INFO::Done
2024-05-20 22:29:16.412802 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:16.416783 INFO::Starting hierarchical adjustment
2024-05-20 22:29:16.417681 INFO::Found 2 batches.
2024-05-20 22:29:16.418395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:16.419162 INFO::Using default BPPARAM
2024-05-20 22:29:16.419855 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:16.42092 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:16.432663 INFO::Done
2024-05-20 22:29:16.433533 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:16.43645 INFO::ASW Batch was 0.521983222152801 prior to batch effect correction and is now -0.000937092499240549 .
2024-05-20 22:29:16.437219 INFO::ASW Label was 0.521871460172333 prior to batch effect correction and is now 0.911996103471856 .
2024-05-20 22:29:16.438145 INFO::Total function execution time is 0.03621506690979 s and adjustment time is 0.0151071548461914 s ( 41.72 )
2024-05-20 22:29:16.439074 INFO::Formatting Data.
2024-05-20 22:29:16.439892 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:16.440896 INFO::Removing potential empty rows and columns
2024-05-20 22:29:16.441971 INFO::Found 0 missing values.
2024-05-20 22:29:16.444319 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:16.44503 INFO::Done
2024-05-20 22:29:16.445741 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:16.448643 INFO::Starting hierarchical adjustment
2024-05-20 22:29:16.44952 INFO::Found 2 batches.
2024-05-20 22:29:16.450219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:16.450977 INFO::Using default BPPARAM
2024-05-20 22:29:16.451671 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:16.452718 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:16.464565 INFO::Done
2024-05-20 22:29:16.465433 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:16.468457 INFO::ASW Batch was 0.521983222152801 prior to batch effect correction and is now -0.000937092499240549 .
2024-05-20 22:29:16.46923 INFO::ASW Label was 0.521871460172333 prior to batch effect correction and is now 0.911996103471856 .
2024-05-20 22:29:16.470185 INFO::Total function execution time is 0.031109094619751 s and adjustment time is 0.0151569843292236 s ( 48.72 )
2024-05-20 22:29:16.485777 INFO::Formatting Data.
2024-05-20 22:29:16.486761 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:16.487804 INFO::Removing potential empty rows and columns
2024-05-20 22:29:16.488837 INFO::Found 0 missing values.
2024-05-20 22:29:16.490803 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:16.491515 INFO::Done
2024-05-20 22:29:16.492209 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:16.494562 INFO::Starting hierarchical adjustment
2024-05-20 22:29:16.495622 INFO::Found 2 batches.
2024-05-20 22:29:16.4965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:16.49737 INFO::Using default BPPARAM
2024-05-20 22:29:16.498075 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:16.499125 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:16.524289 INFO::Done
2024-05-20 22:29:16.52517 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:16.527204 INFO::ASW Batch was 0.0613592441331066 prior to batch effect correction and is now -0.044939243524915 .
2024-05-20 22:29:16.528173 INFO::Total function execution time is 0.042590856552124 s and adjustment time is 0.0287728309631348 s ( 67.56 )
2024-05-20 22:29:16.543769 INFO::Formatting Data.
2024-05-20 22:29:16.544737 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:16.545816 INFO::Removing potential empty rows and columns
2024-05-20 22:29:16.546933 INFO::Found 0 missing values.
2024-05-20 22:29:16.548144 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.
2024-05-20 22:29:16.551969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:16.552682 INFO::Done
2024-05-20 22:29:16.553376 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:16.556325 INFO::Starting hierarchical adjustment
2024-05-20 22:29:16.557215 INFO::Found 2 batches.
2024-05-20 22:29:16.557927 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:16.558697 INFO::Using default BPPARAM
2024-05-20 22:29:16.559396 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:16.560442 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:16.573766 INFO::Done
2024-05-20 22:29:16.574623 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:16.577561 INFO::ASW Batch was 0.462256042075833 prior to batch effect correction and is now 0.00350302279386807 .
2024-05-20 22:29:16.578329 INFO::ASW Label was 0.557263630102108 prior to batch effect correction and is now 0.913455376279923 .
2024-05-20 22:29:16.579255 INFO::Total function execution time is 0.0355780124664307 s and adjustment time is 0.0166580677032471 s ( 46.82 )
2024-05-20 22:29:16.580185 INFO::Formatting Data.
2024-05-20 22:29:16.581024 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:16.582064 INFO::Removing potential empty rows and columns
2024-05-20 22:29:16.58317 INFO::Found 0 missing values.
2024-05-20 22:29:16.584215 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.
2024-05-20 22:29:16.588057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:16.588787 INFO::Done
2024-05-20 22:29:16.589486 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:16.592733 INFO::Starting hierarchical adjustment
2024-05-20 22:29:16.59361 INFO::Found 2 batches.
2024-05-20 22:29:16.594318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:16.595102 INFO::Using default BPPARAM
2024-05-20 22:29:16.595844 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:16.596921 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:16.61123 INFO::Done
2024-05-20 22:29:16.612147 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:16.615192 INFO::ASW Batch was 0.462256042075833 prior to batch effect correction and is now 0.00350302279386807 .
2024-05-20 22:29:16.615989 INFO::ASW Label was 0.557263630102108 prior to batch effect correction and is now 0.913455376279923 .
2024-05-20 22:29:16.616944 INFO::Total function execution time is 0.0367641448974609 s and adjustment time is 0.0177159309387207 s ( 48.19 )
2024-05-20 22:29:16.915884 INFO::Formatting Data.
2024-05-20 22:29:16.917508 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:16.919305 INFO::Removing potential empty rows and columns
2024-05-20 22:29:16.92124 INFO::Found 0 missing values.
2024-05-20 22:29:16.926064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:16.927324 INFO::Done
2024-05-20 22:29:16.928567 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:16.932171 INFO::Starting hierarchical adjustment
2024-05-20 22:29:16.933755 INFO::Found 3 batches.
2024-05-20 22:29:16.93506 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:16.936515 INFO::Using default BPPARAM
2024-05-20 22:29:16.937853 INFO::Processing subtree level 1
2024-05-20 22:29:19.744041 INFO::Adjusting the last 1 batches sequentially
2024-05-20 22:29:19.746063 INFO::Done
2024-05-20 22:29:19.74715 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:19.749242 INFO::ASW Batch was -0.0673643460053159 prior to batch effect correction and is now -0.0673643460053159 .
2024-05-20 22:29:19.75023 INFO::Total function execution time is 2.8345730304718 s and adjustment time is 2.81254911422729 s ( 99.22 )
2024-05-20 22:29:19.751293 INFO::Formatting Data.
2024-05-20 22:29:19.752085 INFO::Typecasting input to dataframe.
2024-05-20 22:29:19.752983 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:19.754006 INFO::Removing potential empty rows and columns
2024-05-20 22:29:19.755187 INFO::Found 0 missing values.
2024-05-20 22:29:19.758143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:19.75895 INFO::Done
2024-05-20 22:29:19.759679 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:19.761868 INFO::Starting hierarchical adjustment
2024-05-20 22:29:19.762732 INFO::Found 3 batches.
2024-05-20 22:29:19.763431 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:19.764196 INFO::Using default BPPARAM
2024-05-20 22:29:19.764923 INFO::Processing subtree level 1
2024-05-20 22:29:22.527348 INFO::Adjusting the last 1 batches sequentially
2024-05-20 22:29:22.529559 INFO::Done
2024-05-20 22:29:22.531052 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:22.533902 INFO::ASW Batch was -0.0673643460053159 prior to batch effect correction and is now -0.0673643460053159 .
2024-05-20 22:29:22.535139 INFO::Total function execution time is 2.78378105163574 s and adjustment time is 2.76687788963318 s ( 99.39 )
2024-05-20 22:29:22.558554 INFO::Formatting Data.
2024-05-20 22:29:22.560119 INFO::Typecasting input to dataframe.
2024-05-20 22:29:22.561788 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:22.563495 INFO::Removing potential empty rows and columns
2024-05-20 22:29:22.565411 INFO::Found 0 missing values.
2024-05-20 22:29:22.569891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:22.571108 INFO::Done
2024-05-20 22:29:22.572351 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:22.575105 INFO::Starting hierarchical adjustment
2024-05-20 22:29:22.57599 INFO::Found 3 batches.
2024-05-20 22:29:22.576699 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:22.577475 INFO::Using default BPPARAM
2024-05-20 22:29:22.578178 INFO::Processing subtree level 1
2024-05-20 22:29:25.085681 INFO::Adjusting the last 1 batches sequentially
2024-05-20 22:29:25.087929 INFO::Done
2024-05-20 22:29:25.089199 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:25.092303 INFO::ASW Batch was -0.183859615609288 prior to batch effect correction and is now -0.183859615609288 .
2024-05-20 22:29:25.093803 INFO::Total function execution time is 2.53538513183594 s and adjustment time is 2.51201701164246 s ( 99.08 )
2024-05-20 22:29:27.803294 INFO::Formatting Data.
2024-05-20 22:29:27.804299 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:27.805536 INFO::Removing potential empty rows and columns
2024-05-20 22:29:27.807806 INFO::Found 1000 missing values.
2024-05-20 22:29:27.821271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:27.822137 INFO::Done
2024-05-20 22:29:27.822876 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:27.82893 INFO::Starting hierarchical adjustment
2024-05-20 22:29:27.82986 INFO::Found 10 batches.
2024-05-20 22:29:27.830573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:27.831695 INFO::Using default BPPARAM
2024-05-20 22:29:27.832895 INFO::Processing subtree level 1
2024-05-20 22:29:30.693131 INFO::Processing subtree level 2
2024-05-20 22:29:33.552762 INFO::Adjusting the last 1 batches sequentially
2024-05-20 22:29:33.554531 INFO::Done
2024-05-20 22:29:33.555757 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:33.562939 INFO::ASW Batch was 0.545158330366433 prior to batch effect correction and is now 0.545158330366433 .
2024-05-20 22:29:33.563834 INFO::ASW Label was 0.279457905000969 prior to batch effect correction and is now 0.279457905000969 .
2024-05-20 22:29:33.564917 INFO::Total function execution time is 5.76171684265137 s and adjustment time is 5.72478604316711 s ( 99.36 )
2024-05-20 22:29:33.565883 INFO::Formatting Data.
2024-05-20 22:29:33.566733 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:33.568145 INFO::Removing potential empty rows and columns
2024-05-20 22:29:33.570457 INFO::Found 1000 missing values.
2024-05-20 22:29:33.583274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:33.584204 INFO::Done
2024-05-20 22:29:33.584965 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:33.591028 INFO::Starting hierarchical adjustment
2024-05-20 22:29:33.592004 INFO::Found 10 batches.
2024-05-20 22:29:34.230014 INFO::Set up parallel execution backend with 2 workers
2024-05-20 22:29:34.231008 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-20 22:29:37.186399 INFO::Adjusting the last 2 batches sequentially
2024-05-20 22:29:37.188608 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-20 22:29:37.21391 INFO::Done
2024-05-20 22:29:37.215401 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:37.224918 INFO::ASW Batch was 0.545158330366433 prior to batch effect correction and is now 0.545158330366433 .
2024-05-20 22:29:37.226343 INFO::ASW Label was 0.279457905000969 prior to batch effect correction and is now 0.279457905000969 .
2024-05-20 22:29:37.227993 INFO::Total function execution time is 3.66205596923828 s and adjustment time is 3.62196016311646 s ( 98.91 )
2024-05-20 22:29:40.155136 INFO::Formatting Data.
2024-05-20 22:29:40.15654 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:40.15815 INFO::Removing potential empty rows and columns
2024-05-20 22:29:40.159481 INFO::Found 0 missing values.
2024-05-20 22:29:40.163829 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:40.164563 INFO::Done
2024-05-20 22:29:40.165524 INFO::Acquiring quality metrics before batch effect correction.
2024-05-20 22:29:40.16985 INFO::Starting hierarchical adjustment
2024-05-20 22:29:40.171293 INFO::Found 3 batches.
2024-05-20 22:29:40.172493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-20 22:29:40.173816 INFO::Using default BPPARAM
2024-05-20 22:29:40.175031 INFO::Processing subtree level 1
2024-05-20 22:29:43.101824 INFO::Adjusting the last 1 batches sequentially
2024-05-20 22:29:43.104054 INFO::Done
2024-05-20 22:29:43.105342 INFO::Acquiring quality metrics after batch effect correction.
2024-05-20 22:29:43.109322 INFO::ASW Batch was 0.26551626631571 prior to batch effect correction and is now -0.115333221544138 .
2024-05-20 22:29:43.110499 INFO::ASW Label was -0.220419958582256 prior to batch effect correction and is now -0.105689123439871 .
2024-05-20 22:29:43.11191 INFO::Total function execution time is 2.95688819885254 s and adjustment time is 2.93295192718506 s ( 99.19 )
2024-05-20 22:29:43.280046 INFO::Formatting Data.
2024-05-20 22:29:43.281087 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:43.282156 INFO::Removing potential empty rows and columns
2024-05-20 22:29:43.283259 INFO::Found 2 missing values.
2024-05-20 22:29:43.285758 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:43.286473 INFO::Done
2024-05-20 22:29:43.341373 INFO::Found NA in Reference column
2024-05-20 22:29:43.361832 INFO::Require at least two references per batch.
2024-05-20 22:29:43.393081 INFO::Formatting Data.
2024-05-20 22:29:43.394038 INFO::Recognized SummarizedExperiment
2024-05-20 22:29:43.394777 INFO::Typecasting input to dataframe.
2024-05-20 22:29:43.402978 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:43.40441 INFO::Removing potential empty rows and columns
2024-05-20 22:29:43.407121 INFO::Found 0 missing values.
2024-05-20 22:29:43.412281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:43.413037 INFO::Done
2024-05-20 22:29:43.428529 INFO::Formatting Data.
2024-05-20 22:29:43.429508 INFO::Recognized SummarizedExperiment
2024-05-20 22:29:43.430261 INFO::Typecasting input to dataframe.
2024-05-20 22:29:43.44565 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:43.447074 INFO::Removing potential empty rows and columns
2024-05-20 22:29:43.45006 INFO::Found 0 missing values.
2024-05-20 22:29:43.458386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:43.459185 INFO::Done
2024-05-20 22:29:43.481366 INFO::Formatting Data.
2024-05-20 22:29:43.482327 INFO::Recognized SummarizedExperiment
2024-05-20 22:29:43.483083 INFO::Typecasting input to dataframe.
2024-05-20 22:29:43.501073 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:43.502333 INFO::Removing potential empty rows and columns
2024-05-20 22:29:43.503537 INFO::Found 0 missing values.
2024-05-20 22:29:43.504853 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.
2024-05-20 22:29:43.509244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:43.510475 INFO::Done
2024-05-20 22:29:43.531958 INFO::Formatting Data.
2024-05-20 22:29:43.533581 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:43.535363 INFO::Removing potential empty rows and columns
2024-05-20 22:29:43.5373 INFO::Found 0 missing values.
2024-05-20 22:29:43.541808 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:43.543044 INFO::Done
2024-05-20 22:29:43.566286 INFO::Formatting Data.
2024-05-20 22:29:43.567816 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:43.569427 INFO::Removing potential empty rows and columns
2024-05-20 22:29:43.571124 INFO::Found 0 missing values.
2024-05-20 22:29:43.575163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:43.576347 INFO::Done
2024-05-20 22:29:43.615856 INFO::Formatting Data.
2024-05-20 22:29:43.616895 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:43.618096 INFO::Removing potential empty rows and columns
2024-05-20 22:29:43.619324 INFO::Found 1 missing values.
2024-05-20 22:29:43.62176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:43.622533 INFO::Done
2024-05-20 22:29:43.64751 INFO::Formatting Data.
2024-05-20 22:29:43.648514 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:43.649586 INFO::Removing potential empty rows and columns
2024-05-20 22:29:43.650661 INFO::Found 2 missing values.
2024-05-20 22:29:43.651731 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.
2024-05-20 22:29:43.653915 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:43.654646 INFO::Done
2024-05-20 22:29:43.669361 INFO::Formatting Data.
2024-05-20 22:29:43.670363 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:43.671419 INFO::Removing potential empty rows and columns
2024-05-20 22:29:43.672493 INFO::Found 2 missing values.
2024-05-20 22:29:43.674152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:43.674869 INFO::Done
2024-05-20 22:29:43.691255 INFO::Formatting Data.
2024-05-20 22:29:43.692233 INFO::Typecasting input to dataframe.
2024-05-20 22:29:43.693664 INFO::Replacing NaNs with NAs.
2024-05-20 22:29:43.695105 INFO::Removing potential empty rows and columns
2024-05-20 22:29:43.696251 INFO::Found 0 missing values.
2024-05-20 22:29:43.699448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-20 22:29:43.700713 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
26.95 1.56 71.15
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 7.42 | 0.39 | 15.59 | |
| compute_asw | 0.05 | 0.00 | 0.05 | |
| count_existing | 0.04 | 0.00 | 0.03 | |
| generate_data_covariables | 0.01 | 0.00 | 0.02 | |
| generate_dataset | 0.03 | 0.00 | 0.03 | |