Yannis Schumann
| Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 10fd252 |
| git_last_commit_date: 2024-11-20 10:26:09 -0500 (Wed, 20 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:38 -0500 (Mon, 25 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| 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 158/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.3 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | 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: 1.3.3 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.3.3.tar.gz |
| StartedAt: 2024-11-24 22:32:02 -0500 (Sun, 24 Nov 2024) |
| EndedAt: 2024-11-24 22:34:21 -0500 (Sun, 24 Nov 2024) |
| EllapsedTime: 139.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BERT.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.3.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 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 '1.3.3'
* 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 ... WARNING
Undocumented code objects:
'generate_truncated_dataset'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 8.32 0.58 21.58
* 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: 1 WARNING
See
'E:/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck/00check.log'
for details.
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
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")
2024-11-24 22:33:10.743695 INFO::Formatting Data.
2024-11-24 22:33:10.746665 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:10.762885 INFO::Removing potential empty rows and columns
2024-11-24 22:33:11.483408 INFO::Found 0 missing values.
2024-11-24 22:33:11.488192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:11.489497 INFO::Done
2024-11-24 22:33:11.490682 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:11.509864 INFO::Starting hierarchical adjustment
2024-11-24 22:33:11.51141 INFO::Found 3 batches.
2024-11-24 22:33:11.512563 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:11.514358 INFO::Using default BPPARAM
2024-11-24 22:33:11.515448 INFO::Processing subtree level 1
2024-11-24 22:33:14.196137 INFO::Adjusting the last 1 batches sequentially
2024-11-24 22:33:14.198167 INFO::Done
2024-11-24 22:33:14.199353 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:14.202367 INFO::ASW Batch was 0.00941756987199378 prior to batch effect correction and is now 0.00941756987199378 .
2024-11-24 22:33:14.203934 INFO::Total function execution time is 3.4609169960022 s and adjustment time is 2.68700504302979 s ( 77.64 )
2024-11-24 22:33:14.224907 INFO::Formatting Data.
2024-11-24 22:33:14.22588 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:14.226968 INFO::Removing potential empty rows and columns
2024-11-24 22:33:14.228123 INFO::Found 0 missing values.
2024-11-24 22:33:14.229174 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.
2024-11-24 22:33:14.237435 INFO::Formatting Data.
2024-11-24 22:33:14.238327 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:14.239387 INFO::Removing potential empty rows and columns
2024-11-24 22:33:14.240585 INFO::Found 0 missing values.
2024-11-24 22:33:14.241628 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.
2024-11-24 22:33:14.25722 INFO::Formatting Data.
2024-11-24 22:33:14.258162 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:14.259193 INFO::Removing potential empty rows and columns
2024-11-24 22:33:14.260295 INFO::Found 0 missing values.
2024-11-24 22:33:14.261341 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.
2024-11-24 22:33:14.264971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:14.265689 INFO::Done
2024-11-24 22:33:14.266374 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:14.268398 INFO::Starting hierarchical adjustment
2024-11-24 22:33:14.269284 INFO::Found 2 batches.
2024-11-24 22:33:14.270065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:14.270839 INFO::Using default BPPARAM
2024-11-24 22:33:14.27154 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:14.272599 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:14.288944 INFO::Done
2024-11-24 22:33:14.290033 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:14.292406 INFO::ASW Batch was 0.198546862413871 prior to batch effect correction and is now -0.1227886223534 .
2024-11-24 22:33:14.293457 INFO::Total function execution time is 0.0363030433654785 s and adjustment time is 0.0197088718414307 s ( 54.29 )
2024-11-24 22:33:14.296549 INFO::Formatting Data.
2024-11-24 22:33:14.29749 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:14.305163 INFO::Formatting Data.
2024-11-24 22:33:14.306218 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:14.307319 INFO::Removing potential empty rows and columns
2024-11-24 22:33:14.30858 INFO::Found 0 missing values.
2024-11-24 22:33:14.311067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:14.311772 INFO::Done
2024-11-24 22:33:14.312438 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:14.314457 INFO::Starting hierarchical adjustment
2024-11-24 22:33:14.315311 INFO::Found 2 batches.
2024-11-24 22:33:14.315984 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:14.316776 INFO::Using default BPPARAM
2024-11-24 22:33:14.317455 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:14.318546 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:14.330654 INFO::Done
2024-11-24 22:33:14.331505 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:14.333597 INFO::ASW Batch was 0.025471766831839 prior to batch effect correction and is now -0.127027637235501 .
2024-11-24 22:33:14.334556 INFO::Total function execution time is 0.0294561386108398 s and adjustment time is 0.0154550075531006 s ( 52.47 )
2024-11-24 22:33:14.335837 INFO::Formatting Data.
2024-11-24 22:33:14.336645 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:14.337646 INFO::Removing potential empty rows and columns
2024-11-24 22:33:14.338738 INFO::Found 0 missing values.
2024-11-24 22:33:14.341209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:14.341922 INFO::Done
2024-11-24 22:33:14.342588 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:14.344614 INFO::Starting hierarchical adjustment
2024-11-24 22:33:14.345477 INFO::Found 2 batches.
2024-11-24 22:33:14.346152 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:14.346945 INFO::Using default BPPARAM
2024-11-24 22:33:14.347629 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:14.348683 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:14.360803 INFO::Done
2024-11-24 22:33:14.361676 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:14.363747 INFO::ASW Batch was 0.025471766831839 prior to batch effect correction and is now -0.127027637235501 .
2024-11-24 22:33:14.364721 INFO::Total function execution time is 0.0288548469543457 s and adjustment time is 0.015427827835083 s ( 53.47 )
2024-11-24 22:33:17.393163 INFO::Formatting Data.
2024-11-24 22:33:17.394747 INFO::Recognized SummarizedExperiment
2024-11-24 22:33:17.396145 INFO::Typecasting input to dataframe.
2024-11-24 22:33:17.445238 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:17.447451 INFO::Removing potential empty rows and columns
2024-11-24 22:33:17.453145 INFO::Found 0 missing values.
2024-11-24 22:33:17.463575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:17.465085 INFO::Done
2024-11-24 22:33:17.466301 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:17.4724 INFO::Starting hierarchical adjustment
2024-11-24 22:33:17.474006 INFO::Found 2 batches.
2024-11-24 22:33:17.475295 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:17.477386 INFO::Using default BPPARAM
2024-11-24 22:33:17.478637 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:17.480739 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:17.566303 INFO::Done
2024-11-24 22:33:17.567619 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:17.573593 INFO::ASW Batch was -0.00428189234328034 prior to batch effect correction and is now -0.0874944434413429 .
2024-11-24 22:33:17.575198 INFO::Total function execution time is 0.18252420425415 s and adjustment time is 0.0925238132476807 s ( 50.69 )
2024-11-24 22:33:17.609251 INFO::Formatting Data.
2024-11-24 22:33:17.610868 INFO::Recognized SummarizedExperiment
2024-11-24 22:33:17.612302 INFO::Typecasting input to dataframe.
2024-11-24 22:33:17.628727 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:17.631244 INFO::Removing potential empty rows and columns
2024-11-24 22:33:17.637604 INFO::Found 0 missing values.
2024-11-24 22:33:17.649468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:17.651143 INFO::Done
2024-11-24 22:33:17.652673 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:17.659343 INFO::Starting hierarchical adjustment
2024-11-24 22:33:17.661006 INFO::Found 2 batches.
2024-11-24 22:33:17.662304 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:17.663586 INFO::Using default BPPARAM
2024-11-24 22:33:17.664858 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:17.667071 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:17.703476 INFO::Done
2024-11-24 22:33:17.704934 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:17.71122 INFO::ASW Batch was -0.00998010998534563 prior to batch effect correction and is now -0.00998010998534563 .
2024-11-24 22:33:17.713 INFO::Total function execution time is 0.103755950927734 s and adjustment time is 0.0427041053771973 s ( 41.16 )
2024-11-24 22:33:17.740639 INFO::Formatting Data.
2024-11-24 22:33:17.741703 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:17.742855 INFO::Removing potential empty rows and columns
2024-11-24 22:33:17.744078 INFO::Found 0 missing values.
2024-11-24 22:33:17.74738 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:17.748173 INFO::Done
2024-11-24 22:33:17.748959 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:17.751205 INFO::Starting hierarchical adjustment
2024-11-24 22:33:17.752159 INFO::Found 3 batches.
2024-11-24 22:33:17.75291 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:17.753698 INFO::Using default BPPARAM
2024-11-24 22:33:17.754419 INFO::Processing subtree level 1
2024-11-24 22:33:27.469358 INFO::Adjusting the last 1 batches sequentially
2024-11-24 22:33:27.471525 INFO::Done
2024-11-24 22:33:27.472765 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:27.475684 INFO::ASW Batch was -0.124624595488882 prior to batch effect correction and is now -0.17666735024509 .
2024-11-24 22:33:27.477072 INFO::Total function execution time is 9.7364981174469 s and adjustment time is 9.71947598457336 s ( 99.83 )
2024-11-24 22:33:27.499326 INFO::Skipping initial DF formatting
2024-11-24 22:33:27.500591 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:27.506766 INFO::Starting hierarchical adjustment
2024-11-24 22:33:27.50818 INFO::Found 5 batches.
2024-11-24 22:33:27.509263 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:27.510357 INFO::Using default BPPARAM
2024-11-24 22:33:27.511321 INFO::Processing subtree level 1
2024-11-24 22:33:30.45352 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:30.455669 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:30.478528 INFO::Done
2024-11-24 22:33:30.479547 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:30.485899 INFO::ASW Batch was 0.495018771734116 prior to batch effect correction and is now 0.495018771734116 .
2024-11-24 22:33:30.487238 INFO::ASW Label was 0.367050853473295 prior to batch effect correction and is now 0.367050853473295 .
2024-11-24 22:33:30.488722 INFO::Total function execution time is 2.98951601982117 s and adjustment time is 2.97053599357605 s ( 99.37 )
2024-11-24 22:33:30.5154 INFO::Formatting Data.
2024-11-24 22:33:30.517066 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:30.518921 INFO::Removing potential empty rows and columns
2024-11-24 22:33:30.52084 INFO::Found 0 missing values.
2024-11-24 22:33:30.527041 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:30.528479 INFO::Done
2024-11-24 22:33:30.52981 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:30.534989 INFO::Starting hierarchical adjustment
2024-11-24 22:33:30.53665 INFO::Found 5 batches.
2024-11-24 22:33:30.537947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:30.539306 INFO::Using default BPPARAM
2024-11-24 22:33:30.54055 INFO::Processing subtree level 1
2024-11-24 22:33:33.604839 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:33.606756 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:33.619875 INFO::Done
2024-11-24 22:33:33.621158 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:33.625602 INFO::ASW Batch was 0.523601101301829 prior to batch effect correction and is now -0.0925162441854861 .
2024-11-24 22:33:33.626817 INFO::ASW Label was 0.21305211850967 prior to batch effect correction and is now 0.757669807427418 .
2024-11-24 22:33:33.628261 INFO::Total function execution time is 3.11299419403076 s and adjustment time is 3.08348512649536 s ( 99.05 )
2024-11-24 22:33:33.629294 INFO::Formatting Data.
2024-11-24 22:33:33.630137 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:33.631219 INFO::Removing potential empty rows and columns
2024-11-24 22:33:33.632354 INFO::Found 0 missing values.
2024-11-24 22:33:33.635978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:33.636749 INFO::Done
2024-11-24 22:33:33.637467 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:33.640542 INFO::Starting hierarchical adjustment
2024-11-24 22:33:33.641462 INFO::Found 5 batches.
2024-11-24 22:33:33.642176 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:33.642905 INFO::Using default BPPARAM
2024-11-24 22:33:33.64356 INFO::Processing subtree level 1
2024-11-24 22:33:36.754277 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:36.756257 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:36.775647 INFO::Done
2024-11-24 22:33:36.777026 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:36.781646 INFO::ASW Batch was 0.523601101301829 prior to batch effect correction and is now -0.0925162441854861 .
2024-11-24 22:33:36.782899 INFO::ASW Label was 0.21305211850967 prior to batch effect correction and is now 0.757669807427418 .
2024-11-24 22:33:36.784337 INFO::Total function execution time is 3.15498089790344 s and adjustment time is 3.13425087928772 s ( 99.34 )
2024-11-24 22:33:36.80637 INFO::Formatting Data.
2024-11-24 22:33:36.807819 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:36.809481 INFO::Removing potential empty rows and columns
2024-11-24 22:33:36.811132 INFO::Found 0 missing values.
2024-11-24 22:33:36.816634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:36.81779 INFO::Done
2024-11-24 22:33:36.818867 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:36.823338 INFO::Starting hierarchical adjustment
2024-11-24 22:33:36.82472 INFO::Found 5 batches.
2024-11-24 22:33:36.825769 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:36.826891 INFO::Using default BPPARAM
2024-11-24 22:33:36.828046 INFO::Processing subtree level 1
2024-11-24 22:33:39.979843 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:39.981437 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:39.996263 INFO::Done
2024-11-24 22:33:39.997113 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:39.999934 INFO::ASW Batch was 0.385261680844621 prior to batch effect correction and is now -0.0944128342453728 .
2024-11-24 22:33:40.000664 INFO::ASW Label was 0.392585139049983 prior to batch effect correction and is now 0.836149956716094 .
2024-11-24 22:33:40.00158 INFO::Total function execution time is 3.19538998603821 s and adjustment time is 3.17177796363831 s ( 99.26 )
2024-11-24 22:33:40.00249 INFO::Formatting Data.
2024-11-24 22:33:40.003246 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:40.004185 INFO::Removing potential empty rows and columns
2024-11-24 22:33:40.00519 INFO::Found 0 missing values.
2024-11-24 22:33:40.008485 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:40.009227 INFO::Done
2024-11-24 22:33:40.009974 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:40.014227 INFO::Starting hierarchical adjustment
2024-11-24 22:33:40.01566 INFO::Found 5 batches.
2024-11-24 22:33:40.016779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:40.018007 INFO::Using default BPPARAM
2024-11-24 22:33:40.019115 INFO::Processing subtree level 1
2024-11-24 22:33:43.087878 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:43.090089 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:43.108255 INFO::Done
2024-11-24 22:33:43.109611 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:43.114243 INFO::ASW Batch was 0.385261680844621 prior to batch effect correction and is now -0.0944128342453728 .
2024-11-24 22:33:43.11552 INFO::ASW Label was 0.392585139049983 prior to batch effect correction and is now 0.836149956716094 .
2024-11-24 22:33:43.116974 INFO::Total function execution time is 3.11442112922668 s and adjustment time is 3.09278798103333 s ( 99.31 )
2024-11-24 22:33:43.1339 INFO::Formatting Data.
2024-11-24 22:33:43.134949 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:43.136012 INFO::Removing potential empty rows and columns
2024-11-24 22:33:43.137703 INFO::Found 0 missing values.
2024-11-24 22:33:43.140756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:43.141602 INFO::Done
2024-11-24 22:33:43.142277 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:43.145642 INFO::Starting hierarchical adjustment
2024-11-24 22:33:43.147057 INFO::Found 2 batches.
2024-11-24 22:33:43.148194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:43.149419 INFO::Using default BPPARAM
2024-11-24 22:33:43.150551 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:43.152265 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:43.167763 INFO::Done
2024-11-24 22:33:43.168654 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:43.171618 INFO::ASW Batch was 0.500497843844006 prior to batch effect correction and is now 0.141920981414226 .
2024-11-24 22:33:43.17238 INFO::ASW Label was 0.579493484355765 prior to batch effect correction and is now 0.844187164491134 .
2024-11-24 22:33:43.173396 INFO::Total function execution time is 0.0395820140838623 s and adjustment time is 0.0209522247314453 s ( 52.93 )
2024-11-24 22:33:43.174288 INFO::Formatting Data.
2024-11-24 22:33:43.175032 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:43.175997 INFO::Removing potential empty rows and columns
2024-11-24 22:33:43.177083 INFO::Found 0 missing values.
2024-11-24 22:33:43.179592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:43.180269 INFO::Done
2024-11-24 22:33:43.180918 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:43.183765 INFO::Starting hierarchical adjustment
2024-11-24 22:33:43.184703 INFO::Found 2 batches.
2024-11-24 22:33:43.185384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:43.186204 INFO::Using default BPPARAM
2024-11-24 22:33:43.186921 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:43.187958 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:43.200559 INFO::Done
2024-11-24 22:33:43.201427 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:43.204962 INFO::ASW Batch was 0.500497843844006 prior to batch effect correction and is now 0.141920981414226 .
2024-11-24 22:33:43.205721 INFO::ASW Label was 0.579493484355765 prior to batch effect correction and is now 0.844187164491134 .
2024-11-24 22:33:43.206639 INFO::Total function execution time is 0.0323610305786133 s and adjustment time is 0.0160260200500488 s ( 49.52 )
2024-11-24 22:33:43.220764 INFO::Formatting Data.
2024-11-24 22:33:43.221712 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:43.222758 INFO::Removing potential empty rows and columns
2024-11-24 22:33:43.223773 INFO::Found 0 missing values.
2024-11-24 22:33:43.225721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:43.2264 INFO::Done
2024-11-24 22:33:43.227054 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:43.229018 INFO::Starting hierarchical adjustment
2024-11-24 22:33:43.229869 INFO::Found 2 batches.
2024-11-24 22:33:43.230595 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:43.23141 INFO::Using default BPPARAM
2024-11-24 22:33:43.2321 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:43.233108 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:43.256751 INFO::Done
2024-11-24 22:33:43.257604 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:43.25966 INFO::ASW Batch was 0.0332671247757735 prior to batch effect correction and is now -0.165974258786964 .
2024-11-24 22:33:43.260609 INFO::Total function execution time is 0.0399341583251953 s and adjustment time is 0.0269839763641357 s ( 67.57 )
2024-11-24 22:33:43.276123 INFO::Formatting Data.
2024-11-24 22:33:43.277337 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:43.27876 INFO::Removing potential empty rows and columns
2024-11-24 22:33:43.280069 INFO::Found 0 missing values.
2024-11-24 22:33:43.28164 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.
2024-11-24 22:33:43.286179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:43.286893 INFO::Done
2024-11-24 22:33:43.287556 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:43.290567 INFO::Starting hierarchical adjustment
2024-11-24 22:33:43.291446 INFO::Found 2 batches.
2024-11-24 22:33:43.292128 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:43.292861 INFO::Using default BPPARAM
2024-11-24 22:33:43.293516 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:43.294644 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:43.307842 INFO::Done
2024-11-24 22:33:43.308738 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:43.31217 INFO::ASW Batch was 0.397652115987989 prior to batch effect correction and is now 0.160728123969644 .
2024-11-24 22:33:43.312998 INFO::ASW Label was 0.698947235096073 prior to batch effect correction and is now 0.824990492648368 .
2024-11-24 22:33:43.313983 INFO::Total function execution time is 0.0380058288574219 s and adjustment time is 0.0165200233459473 s ( 43.47 )
2024-11-24 22:33:43.314923 INFO::Formatting Data.
2024-11-24 22:33:43.315747 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:43.316861 INFO::Removing potential empty rows and columns
2024-11-24 22:33:43.31802 INFO::Found 0 missing values.
2024-11-24 22:33:43.319122 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.
2024-11-24 22:33:43.323507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:43.324278 INFO::Done
2024-11-24 22:33:43.325055 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:43.328056 INFO::Starting hierarchical adjustment
2024-11-24 22:33:43.328961 INFO::Found 2 batches.
2024-11-24 22:33:43.329676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:43.330406 INFO::Using default BPPARAM
2024-11-24 22:33:43.331092 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:33:43.332131 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:33:43.346697 INFO::Done
2024-11-24 22:33:43.347614 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:43.351024 INFO::ASW Batch was 0.397652115987989 prior to batch effect correction and is now 0.160728123969644 .
2024-11-24 22:33:43.351788 INFO::ASW Label was 0.698947235096073 prior to batch effect correction and is now 0.824990492648368 .
2024-11-24 22:33:43.352695 INFO::Total function execution time is 0.037787914276123 s and adjustment time is 0.0178511142730713 s ( 47.24 )
2024-11-24 22:33:43.552472 INFO::Formatting Data.
2024-11-24 22:33:43.553964 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:43.555677 INFO::Removing potential empty rows and columns
2024-11-24 22:33:43.557469 INFO::Found 0 missing values.
2024-11-24 22:33:43.561761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:43.56297 INFO::Done
2024-11-24 22:33:43.564123 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:43.567221 INFO::Starting hierarchical adjustment
2024-11-24 22:33:43.568599 INFO::Found 3 batches.
2024-11-24 22:33:43.569724 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:43.570917 INFO::Using default BPPARAM
2024-11-24 22:33:43.572039 INFO::Processing subtree level 1
2024-11-24 22:33:46.472104 INFO::Adjusting the last 1 batches sequentially
2024-11-24 22:33:46.474157 INFO::Done
2024-11-24 22:33:46.475384 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:46.478377 INFO::ASW Batch was -0.0947652151695879 prior to batch effect correction and is now -0.0947652151695879 .
2024-11-24 22:33:46.479756 INFO::Total function execution time is 2.92740511894226 s and adjustment time is 2.90576386451721 s ( 99.26 )
2024-11-24 22:33:46.481316 INFO::Formatting Data.
2024-11-24 22:33:46.482489 INFO::Typecasting input to dataframe.
2024-11-24 22:33:46.483785 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:46.485259 INFO::Removing potential empty rows and columns
2024-11-24 22:33:46.486857 INFO::Found 0 missing values.
2024-11-24 22:33:46.490767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:46.491864 INFO::Done
2024-11-24 22:33:46.492903 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:46.495958 INFO::Starting hierarchical adjustment
2024-11-24 22:33:46.497287 INFO::Found 3 batches.
2024-11-24 22:33:46.498337 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:46.499477 INFO::Using default BPPARAM
2024-11-24 22:33:46.500575 INFO::Processing subtree level 1
2024-11-24 22:33:49.278493 INFO::Adjusting the last 1 batches sequentially
2024-11-24 22:33:49.280589 INFO::Done
2024-11-24 22:33:49.281702 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:49.28463 INFO::ASW Batch was -0.0947652151695879 prior to batch effect correction and is now -0.0947652151695879 .
2024-11-24 22:33:49.286011 INFO::Total function execution time is 2.8047080039978 s and adjustment time is 2.78349018096924 s ( 99.24 )
2024-11-24 22:33:49.305963 INFO::Formatting Data.
2024-11-24 22:33:49.307328 INFO::Typecasting input to dataframe.
2024-11-24 22:33:49.308828 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:49.31039 INFO::Removing potential empty rows and columns
2024-11-24 22:33:49.312076 INFO::Found 0 missing values.
2024-11-24 22:33:49.315655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:49.316655 INFO::Done
2024-11-24 22:33:49.317654 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:49.320601 INFO::Starting hierarchical adjustment
2024-11-24 22:33:49.321823 INFO::Found 3 batches.
2024-11-24 22:33:49.322804 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:49.323956 INFO::Using default BPPARAM
2024-11-24 22:33:49.325028 INFO::Processing subtree level 1
2024-11-24 22:33:51.986391 INFO::Adjusting the last 1 batches sequentially
2024-11-24 22:33:51.988615 INFO::Done
2024-11-24 22:33:51.989927 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:33:51.993169 INFO::ASW Batch was -0.0207610130430463 prior to batch effect correction and is now -0.0207610130430463 .
2024-11-24 22:33:51.994676 INFO::Total function execution time is 2.68881702423096 s and adjustment time is 2.66694521903992 s ( 99.19 )
2024-11-24 22:33:55.033232 INFO::Formatting Data.
2024-11-24 22:33:55.034182 INFO::Replacing NaNs with NAs.
2024-11-24 22:33:55.035357 INFO::Removing potential empty rows and columns
2024-11-24 22:33:55.037605 INFO::Found 1000 missing values.
2024-11-24 22:33:55.050786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:33:55.051666 INFO::Done
2024-11-24 22:33:55.052361 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:33:55.058747 INFO::Starting hierarchical adjustment
2024-11-24 22:33:55.059813 INFO::Found 10 batches.
2024-11-24 22:33:55.060539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:33:55.061292 INFO::Using default BPPARAM
2024-11-24 22:33:55.062018 INFO::Processing subtree level 1
2024-11-24 22:33:58.030896 INFO::Processing subtree level 2
2024-11-24 22:34:01.140519 INFO::Adjusting the last 1 batches sequentially
2024-11-24 22:34:01.142836 INFO::Done
2024-11-24 22:34:01.144009 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:34:01.152494 INFO::ASW Batch was 0.501172935116353 prior to batch effect correction and is now 0.501172935116353 .
2024-11-24 22:34:01.153729 INFO::ASW Label was 0.317399352230621 prior to batch effect correction and is now 0.317399352230621 .
2024-11-24 22:34:01.155213 INFO::Total function execution time is 6.12200593948364 s and adjustment time is 6.08319306373596 s ( 99.37 )
2024-11-24 22:34:01.156543 INFO::Formatting Data.
2024-11-24 22:34:01.157685 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:01.159386 INFO::Removing potential empty rows and columns
2024-11-24 22:34:01.161514 INFO::Found 1000 missing values.
2024-11-24 22:34:01.177379 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:01.178652 INFO::Done
2024-11-24 22:34:01.179755 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:34:01.187739 INFO::Starting hierarchical adjustment
2024-11-24 22:34:01.188745 INFO::Found 10 batches.
2024-11-24 22:34:01.961779 INFO::Set up parallel execution backend with 2 workers
2024-11-24 22:34:01.963175 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-11-24 22:34:04.903682 INFO::Adjusting the last 2 batches sequentially
2024-11-24 22:34:04.90515 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-24 22:34:04.919557 INFO::Done
2024-11-24 22:34:04.920453 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:34:04.926868 INFO::ASW Batch was 0.501172935116353 prior to batch effect correction and is now 0.501172935116353 .
2024-11-24 22:34:04.927737 INFO::ASW Label was 0.317399352230621 prior to batch effect correction and is now 0.317399352230621 .
2024-11-24 22:34:04.928683 INFO::Total function execution time is 3.77220892906189 s and adjustment time is 3.73095417022705 s ( 98.91 )
2024-11-24 22:34:07.656088 INFO::Formatting Data.
2024-11-24 22:34:07.657078 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:07.658132 INFO::Removing potential empty rows and columns
2024-11-24 22:34:07.659225 INFO::Found 0 missing values.
2024-11-24 22:34:07.662238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:07.662948 INFO::Done
2024-11-24 22:34:07.663609 INFO::Acquiring quality metrics before batch effect correction.
2024-11-24 22:34:07.666221 INFO::Starting hierarchical adjustment
2024-11-24 22:34:07.667057 INFO::Found 3 batches.
2024-11-24 22:34:07.667718 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-24 22:34:07.66845 INFO::Using default BPPARAM
2024-11-24 22:34:07.669106 INFO::Processing subtree level 1
2024-11-24 22:34:10.67021 INFO::Adjusting the last 1 batches sequentially
2024-11-24 22:34:10.672311 INFO::Done
2024-11-24 22:34:10.673543 INFO::Acquiring quality metrics after batch effect correction.
2024-11-24 22:34:10.677407 INFO::ASW Batch was 0.177838573061813 prior to batch effect correction and is now -0.165202304359783 .
2024-11-24 22:34:10.678548 INFO::ASW Label was -0.173423604246094 prior to batch effect correction and is now -0.0328173741316226 .
2024-11-24 22:34:10.679918 INFO::Total function execution time is 3.02387189865112 s and adjustment time is 3.00532412528992 s ( 99.39 )
2024-11-24 22:34:10.856012 INFO::Formatting Data.
2024-11-24 22:34:10.857609 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:10.859454 INFO::Removing potential empty rows and columns
2024-11-24 22:34:10.861326 INFO::Found 2 missing values.
2024-11-24 22:34:10.865891 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:10.867047 INFO::Done
2024-11-24 22:34:10.922124 INFO::Found NA in Reference column
2024-11-24 22:34:10.940338 INFO::Require at least two references per batch.
2024-11-24 22:34:10.970714 INFO::Formatting Data.
2024-11-24 22:34:10.972128 INFO::Recognized SummarizedExperiment
2024-11-24 22:34:10.973317 INFO::Typecasting input to dataframe.
2024-11-24 22:34:10.986024 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:10.988097 INFO::Removing potential empty rows and columns
2024-11-24 22:34:10.992701 INFO::Found 0 missing values.
2024-11-24 22:34:11.000964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:11.002285 INFO::Done
2024-11-24 22:34:11.02334 INFO::Formatting Data.
2024-11-24 22:34:11.024751 INFO::Recognized SummarizedExperiment
2024-11-24 22:34:11.025943 INFO::Typecasting input to dataframe.
2024-11-24 22:34:11.049472 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:11.051404 INFO::Removing potential empty rows and columns
2024-11-24 22:34:11.055832 INFO::Found 0 missing values.
2024-11-24 22:34:11.068774 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:11.070033 INFO::Done
2024-11-24 22:34:11.090928 INFO::Formatting Data.
2024-11-24 22:34:11.092244 INFO::Recognized SummarizedExperiment
2024-11-24 22:34:11.093311 INFO::Typecasting input to dataframe.
2024-11-24 22:34:11.115873 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:11.11761 INFO::Removing potential empty rows and columns
2024-11-24 22:34:11.119422 INFO::Found 0 missing values.
2024-11-24 22:34:11.121048 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.
2024-11-24 22:34:11.127566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:11.128844 INFO::Done
2024-11-24 22:34:11.148775 INFO::Formatting Data.
2024-11-24 22:34:11.150307 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:11.152049 INFO::Removing potential empty rows and columns
2024-11-24 22:34:11.153879 INFO::Found 0 missing values.
2024-11-24 22:34:11.158313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:11.159507 INFO::Done
2024-11-24 22:34:11.180468 INFO::Formatting Data.
2024-11-24 22:34:11.181892 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:11.183445 INFO::Removing potential empty rows and columns
2024-11-24 22:34:11.185117 INFO::Found 0 missing values.
2024-11-24 22:34:11.1894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:11.190473 INFO::Done
2024-11-24 22:34:11.244346 INFO::Formatting Data.
2024-11-24 22:34:11.245871 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:11.247744 INFO::Removing potential empty rows and columns
2024-11-24 22:34:11.249726 INFO::Found 1 missing values.
2024-11-24 22:34:11.253558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:11.254755 INFO::Done
2024-11-24 22:34:11.290656 INFO::Formatting Data.
2024-11-24 22:34:11.29213 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:11.293789 INFO::Removing potential empty rows and columns
2024-11-24 22:34:11.295479 INFO::Found 2 missing values.
2024-11-24 22:34:11.297155 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.
2024-11-24 22:34:11.300511 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:11.301588 INFO::Done
2024-11-24 22:34:11.320494 INFO::Formatting Data.
2024-11-24 22:34:11.321943 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:11.323536 INFO::Removing potential empty rows and columns
2024-11-24 22:34:11.325145 INFO::Found 2 missing values.
2024-11-24 22:34:11.327612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:11.328698 INFO::Done
2024-11-24 22:34:11.348126 INFO::Formatting Data.
2024-11-24 22:34:11.349547 INFO::Typecasting input to dataframe.
2024-11-24 22:34:11.35108 INFO::Replacing NaNs with NAs.
2024-11-24 22:34:11.352631 INFO::Removing potential empty rows and columns
2024-11-24 22:34:11.354324 INFO::Found 0 missing values.
2024-11-24 22:34:11.358322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-24 22:34:11.359393 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 138 ]
>
> proc.time()
user system elapsed
29.78 1.31 76.82
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.32 | 0.58 | 21.58 | |
| compute_asw | 0.05 | 0.00 | 0.04 | |
| count_existing | 0.00 | 0.01 | 0.02 | |
| generate_data_covariables | 0.01 | 0.02 | 0.03 | |
| generate_dataset | 0.02 | 0.00 | 0.01 | |