Yannis Schumann
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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 2024-06-11 15:40 -0400 (Tue, 11 Jun 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" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 154/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.0.tar.gz |
| StartedAt: 2024-06-10 00:02:52 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 00:09:48 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 416.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BERT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 8.86 5.42 30.98
* 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")
2024-06-10 00:05:45.385819 INFO::Formatting Data.
2024-06-10 00:05:45.398495 INFO::Replacing NaNs with NAs.
2024-06-10 00:05:45.407282 INFO::Removing potential empty rows and columns
2024-06-10 00:05:45.890095 INFO::Found 0 missing values.
2024-06-10 00:05:45.893134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:05:45.893955 INFO::Done
2024-06-10 00:05:45.894683 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:05:45.944962 INFO::Starting hierarchical adjustment
2024-06-10 00:05:45.94602 INFO::Found 3 batches.
2024-06-10 00:05:45.94677 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:05:45.948036 INFO::Using default BPPARAM
2024-06-10 00:05:45.948769 INFO::Processing subtree level 1
2024-06-10 00:05:58.613941 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:05:58.61623 INFO::Done
2024-06-10 00:05:58.617515 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:05:58.62055 INFO::ASW Batch was -0.0746508123691724 prior to batch effect correction and is now -0.0746508123691724 .
2024-06-10 00:05:58.622163 INFO::Total function execution time is 13.2367119789124 s and adjustment time is 12.6703369617462 s ( 95.72 )
2024-06-10 00:05:58.641351 INFO::Formatting Data.
2024-06-10 00:05:58.642377 INFO::Replacing NaNs with NAs.
2024-06-10 00:05:58.643455 INFO::Removing potential empty rows and columns
2024-06-10 00:05:58.644603 INFO::Found 0 missing values.
2024-06-10 00:05:58.64573 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.
2024-06-10 00:05:58.65408 INFO::Formatting Data.
2024-06-10 00:05:58.654968 INFO::Replacing NaNs with NAs.
2024-06-10 00:05:58.655984 INFO::Removing potential empty rows and columns
2024-06-10 00:05:58.657083 INFO::Found 0 missing values.
2024-06-10 00:05:58.65812 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.
2024-06-10 00:05:58.674163 INFO::Formatting Data.
2024-06-10 00:05:58.67511 INFO::Replacing NaNs with NAs.
2024-06-10 00:05:58.676207 INFO::Removing potential empty rows and columns
2024-06-10 00:05:58.677327 INFO::Found 0 missing values.
2024-06-10 00:05:58.678404 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.
2024-06-10 00:05:58.682064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:05:58.682776 INFO::Done
2024-06-10 00:05:58.683495 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:05:58.685586 INFO::Starting hierarchical adjustment
2024-06-10 00:05:58.686449 INFO::Found 2 batches.
2024-06-10 00:05:58.687228 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:05:58.68801 INFO::Using default BPPARAM
2024-06-10 00:05:58.688703 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:05:58.689739 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:05:58.705664 INFO::Done
2024-06-10 00:05:58.706532 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:05:58.708561 INFO::ASW Batch was 0.0394824389062149 prior to batch effect correction and is now -0.11447766785804 .
2024-06-10 00:05:58.709513 INFO::Total function execution time is 0.0354239940643311 s and adjustment time is 0.0193121433258057 s ( 54.52 )
2024-06-10 00:05:58.712241 INFO::Formatting Data.
2024-06-10 00:05:58.713032 INFO::Replacing NaNs with NAs.
2024-06-10 00:05:58.719727 INFO::Formatting Data.
2024-06-10 00:05:58.720549 INFO::Replacing NaNs with NAs.
2024-06-10 00:05:58.721545 INFO::Removing potential empty rows and columns
2024-06-10 00:05:58.722636 INFO::Found 0 missing values.
2024-06-10 00:05:58.725048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:05:58.725759 INFO::Done
2024-06-10 00:05:58.726444 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:05:58.728442 INFO::Starting hierarchical adjustment
2024-06-10 00:05:58.729293 INFO::Found 2 batches.
2024-06-10 00:05:58.729983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:05:58.730731 INFO::Using default BPPARAM
2024-06-10 00:05:58.731423 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:05:58.732451 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:05:58.744106 INFO::Done
2024-06-10 00:05:58.744915 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:05:58.746939 INFO::ASW Batch was -0.0449350571816515 prior to batch effect correction and is now -0.124746773506176 .
2024-06-10 00:05:58.747873 INFO::Total function execution time is 0.0281651020050049 s and adjustment time is 0.0149331092834473 s ( 53.02 )
2024-06-10 00:05:58.749005 INFO::Formatting Data.
2024-06-10 00:05:58.749761 INFO::Replacing NaNs with NAs.
2024-06-10 00:05:58.750729 INFO::Removing potential empty rows and columns
2024-06-10 00:05:58.751786 INFO::Found 0 missing values.
2024-06-10 00:05:58.754192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:05:58.754937 INFO::Done
2024-06-10 00:05:58.755623 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:05:58.757594 INFO::Starting hierarchical adjustment
2024-06-10 00:05:58.758435 INFO::Found 2 batches.
2024-06-10 00:05:58.75912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:05:58.759874 INFO::Using default BPPARAM
2024-06-10 00:05:58.760558 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:05:58.761576 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:05:58.773285 INFO::Done
2024-06-10 00:05:58.774098 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:05:58.776136 INFO::ASW Batch was -0.0449350571816515 prior to batch effect correction and is now -0.124746773506176 .
2024-06-10 00:05:58.777068 INFO::Total function execution time is 0.028052806854248 s and adjustment time is 0.0149679183959961 s ( 53.36 )
2024-06-10 00:06:01.229681 INFO::Formatting Data.
2024-06-10 00:06:01.230635 INFO::Recognized SummarizedExperiment
2024-06-10 00:06:01.231385 INFO::Typecasting input to dataframe.
2024-06-10 00:06:01.281289 INFO::Replacing NaNs with NAs.
2024-06-10 00:06:01.282761 INFO::Removing potential empty rows and columns
2024-06-10 00:06:01.28591 INFO::Found 0 missing values.
2024-06-10 00:06:02.086674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:06:02.088218 INFO::Done
2024-06-10 00:06:02.089621 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:06:02.095433 INFO::Starting hierarchical adjustment
2024-06-10 00:06:02.096948 INFO::Found 2 batches.
2024-06-10 00:06:02.098239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:06:02.100187 INFO::Using default BPPARAM
2024-06-10 00:06:02.101359 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:06:02.103211 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:06:02.170764 INFO::Done
2024-06-10 00:06:02.172198 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:06:02.178286 INFO::ASW Batch was -0.011412766190605 prior to batch effect correction and is now -0.087802455949942 .
2024-06-10 00:06:02.179966 INFO::Total function execution time is 0.950483798980713 s and adjustment time is 0.0740039348602295 s ( 7.79 )
2024-06-10 00:06:02.210031 INFO::Formatting Data.
2024-06-10 00:06:02.211576 INFO::Recognized SummarizedExperiment
2024-06-10 00:06:02.212917 INFO::Typecasting input to dataframe.
2024-06-10 00:06:02.225881 INFO::Replacing NaNs with NAs.
2024-06-10 00:06:02.228007 INFO::Removing potential empty rows and columns
2024-06-10 00:06:02.232997 INFO::Found 0 missing values.
2024-06-10 00:06:02.242131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:06:02.243504 INFO::Done
2024-06-10 00:06:02.244819 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:06:02.250876 INFO::Starting hierarchical adjustment
2024-06-10 00:06:02.252284 INFO::Found 2 batches.
2024-06-10 00:06:02.253433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:06:02.254661 INFO::Using default BPPARAM
2024-06-10 00:06:02.255787 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:06:02.257587 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:06:02.293603 INFO::Done
2024-06-10 00:06:02.295086 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:06:02.301508 INFO::ASW Batch was -0.00525790587304762 prior to batch effect correction and is now -0.00525790587304762 .
2024-06-10 00:06:02.303135 INFO::Total function execution time is 0.0930759906768799 s and adjustment time is 0.041471004486084 s ( 44.56 )
2024-06-10 00:06:02.33403 INFO::Formatting Data.
2024-06-10 00:06:02.33552 INFO::Replacing NaNs with NAs.
2024-06-10 00:06:02.337245 INFO::Removing potential empty rows and columns
2024-06-10 00:06:02.339055 INFO::Found 0 missing values.
2024-06-10 00:06:02.343496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:06:02.344649 INFO::Done
2024-06-10 00:06:02.345797 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:06:02.348904 INFO::Starting hierarchical adjustment
2024-06-10 00:06:02.350203 INFO::Found 3 batches.
2024-06-10 00:06:02.351304 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:06:02.352522 INFO::Using default BPPARAM
2024-06-10 00:06:02.353649 INFO::Processing subtree level 1
2024-06-10 00:06:24.054793 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:06:24.057058 INFO::Done
2024-06-10 00:06:24.058342 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:06:24.061389 INFO::ASW Batch was -0.0742886988004085 prior to batch effect correction and is now -0.170375325977803 .
2024-06-10 00:06:24.062863 INFO::Total function execution time is 21.7289409637451 s and adjustment time is 21.7070350646973 s ( 99.9 )
2024-06-10 00:06:24.085411 INFO::Skipping initial DF formatting
2024-06-10 00:06:24.086733 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:06:24.092761 INFO::Starting hierarchical adjustment
2024-06-10 00:06:24.094125 INFO::Found 5 batches.
2024-06-10 00:06:24.095194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:06:24.096333 INFO::Using default BPPARAM
2024-06-10 00:06:24.097386 INFO::Processing subtree level 1
2024-06-10 00:06:37.442959 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:06:37.445145 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:06:37.468487 INFO::Done
2024-06-10 00:06:37.469777 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:06:37.474252 INFO::ASW Batch was 0.574259694486158 prior to batch effect correction and is now 0.574259694486158 .
2024-06-10 00:06:37.475074 INFO::ASW Label was 0.300245447755999 prior to batch effect correction and is now 0.300245447755999 .
2024-06-10 00:06:37.476054 INFO::Total function execution time is 13.3908190727234 s and adjustment time is 13.3745069503784 s ( 99.88 )
2024-06-10 00:06:37.495072 INFO::Formatting Data.
2024-06-10 00:06:37.496071 INFO::Replacing NaNs with NAs.
2024-06-10 00:06:37.497176 INFO::Removing potential empty rows and columns
2024-06-10 00:06:37.498296 INFO::Found 0 missing values.
2024-06-10 00:06:37.501823 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:06:37.502588 INFO::Done
2024-06-10 00:06:37.5033 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:06:37.506345 INFO::Starting hierarchical adjustment
2024-06-10 00:06:37.507229 INFO::Found 5 batches.
2024-06-10 00:06:37.507934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:06:37.50871 INFO::Using default BPPARAM
2024-06-10 00:06:37.509412 INFO::Processing subtree level 1
2024-06-10 00:06:50.808824 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:06:50.810598 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:06:50.828291 INFO::Done
2024-06-10 00:06:50.829749 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:06:50.834765 INFO::ASW Batch was 0.370342372409423 prior to batch effect correction and is now -0.0938647697660915 .
2024-06-10 00:06:50.836134 INFO::ASW Label was 0.369441867876037 prior to batch effect correction and is now 0.930749339084252 .
2024-06-10 00:06:50.837757 INFO::Total function execution time is 13.3426899909973 s and adjustment time is 13.3211119174957 s ( 99.84 )
2024-06-10 00:06:50.839386 INFO::Formatting Data.
2024-06-10 00:06:50.840764 INFO::Replacing NaNs with NAs.
2024-06-10 00:06:50.842522 INFO::Removing potential empty rows and columns
2024-06-10 00:06:50.844405 INFO::Found 0 missing values.
2024-06-10 00:06:50.850825 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:06:50.852162 INFO::Done
2024-06-10 00:06:50.853437 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:06:50.858518 INFO::Starting hierarchical adjustment
2024-06-10 00:06:50.860057 INFO::Found 5 batches.
2024-06-10 00:06:50.861402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:06:50.862854 INFO::Using default BPPARAM
2024-06-10 00:06:50.864191 INFO::Processing subtree level 1
2024-06-10 00:07:04.573993 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:07:04.576066 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:07:04.595623 INFO::Done
2024-06-10 00:07:04.597031 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:07:04.601795 INFO::ASW Batch was 0.370342372409423 prior to batch effect correction and is now -0.0938647697660915 .
2024-06-10 00:07:04.602664 INFO::ASW Label was 0.369441867876037 prior to batch effect correction and is now 0.930749339084252 .
2024-06-10 00:07:04.603994 INFO::Total function execution time is 13.764634847641 s and adjustment time is 13.735771894455 s ( 99.79 )
2024-06-10 00:07:04.628423 INFO::Formatting Data.
2024-06-10 00:07:04.63005 INFO::Replacing NaNs with NAs.
2024-06-10 00:07:04.631807 INFO::Removing potential empty rows and columns
2024-06-10 00:07:04.633622 INFO::Found 0 missing values.
2024-06-10 00:07:04.639446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:07:04.640692 INFO::Done
2024-06-10 00:07:04.641876 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:07:04.646694 INFO::Starting hierarchical adjustment
2024-06-10 00:07:04.648143 INFO::Found 5 batches.
2024-06-10 00:07:04.649333 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:07:04.650612 INFO::Using default BPPARAM
2024-06-10 00:07:04.651791 INFO::Processing subtree level 1
2024-06-10 00:07:18.038376 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:07:18.040338 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:07:18.052476 INFO::Done
2024-06-10 00:07:18.053363 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:07:18.056438 INFO::ASW Batch was 0.505617750228954 prior to batch effect correction and is now -0.0651920820860148 .
2024-06-10 00:07:18.057222 INFO::ASW Label was 0.342581766320604 prior to batch effect correction and is now 0.73022467629549 .
2024-06-10 00:07:18.058168 INFO::Total function execution time is 13.4299359321594 s and adjustment time is 13.4045650959015 s ( 99.81 )
2024-06-10 00:07:18.059118 INFO::Formatting Data.
2024-06-10 00:07:18.059913 INFO::Replacing NaNs with NAs.
2024-06-10 00:07:18.060933 INFO::Removing potential empty rows and columns
2024-06-10 00:07:18.062016 INFO::Found 0 missing values.
2024-06-10 00:07:18.065464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:07:18.06619 INFO::Done
2024-06-10 00:07:18.066884 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:07:18.069881 INFO::Starting hierarchical adjustment
2024-06-10 00:07:18.070822 INFO::Found 5 batches.
2024-06-10 00:07:18.071626 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:07:18.072465 INFO::Using default BPPARAM
2024-06-10 00:07:18.073239 INFO::Processing subtree level 1
2024-06-10 00:07:32.051379 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:07:32.053262 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:07:32.071136 INFO::Done
2024-06-10 00:07:32.072374 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:07:32.076478 INFO::ASW Batch was 0.505617750228954 prior to batch effect correction and is now -0.0651920820860148 .
2024-06-10 00:07:32.077823 INFO::ASW Label was 0.342581766320604 prior to batch effect correction and is now 0.73022467629549 .
2024-06-10 00:07:32.079443 INFO::Total function execution time is 14.020231962204 s and adjustment time is 14.0004060268402 s ( 99.86 )
2024-06-10 00:07:32.098706 INFO::Formatting Data.
2024-06-10 00:07:32.099672 INFO::Replacing NaNs with NAs.
2024-06-10 00:07:32.100751 INFO::Removing potential empty rows and columns
2024-06-10 00:07:32.101855 INFO::Found 0 missing values.
2024-06-10 00:07:32.104216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:07:32.104915 INFO::Done
2024-06-10 00:07:32.105594 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:07:32.108464 INFO::Starting hierarchical adjustment
2024-06-10 00:07:32.109319 INFO::Found 2 batches.
2024-06-10 00:07:32.110012 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:07:32.110768 INFO::Using default BPPARAM
2024-06-10 00:07:32.111449 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:07:32.112484 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:07:32.12394 INFO::Done
2024-06-10 00:07:32.124775 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:07:32.127682 INFO::ASW Batch was 0.736921176712933 prior to batch effect correction and is now 0.0327230158309953 .
2024-06-10 00:07:32.128436 INFO::ASW Label was 0.354224822783582 prior to batch effect correction and is now 0.899976475857652 .
2024-06-10 00:07:32.129367 INFO::Total function execution time is 0.030756950378418 s and adjustment time is 0.0147390365600586 s ( 47.92 )
2024-06-10 00:07:32.130287 INFO::Formatting Data.
2024-06-10 00:07:32.131069 INFO::Replacing NaNs with NAs.
2024-06-10 00:07:32.13211 INFO::Removing potential empty rows and columns
2024-06-10 00:07:32.133187 INFO::Found 0 missing values.
2024-06-10 00:07:32.135532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:07:32.136248 INFO::Done
2024-06-10 00:07:32.136938 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:07:32.139751 INFO::Starting hierarchical adjustment
2024-06-10 00:07:32.140612 INFO::Found 2 batches.
2024-06-10 00:07:32.141308 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:07:32.142061 INFO::Using default BPPARAM
2024-06-10 00:07:32.142747 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:07:32.143795 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:07:32.156746 INFO::Done
2024-06-10 00:07:32.157611 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:07:32.160611 INFO::ASW Batch was 0.736921176712933 prior to batch effect correction and is now 0.0327230158309953 .
2024-06-10 00:07:32.161399 INFO::ASW Label was 0.354224822783582 prior to batch effect correction and is now 0.899976475857652 .
2024-06-10 00:07:32.162333 INFO::Total function execution time is 0.032059907913208 s and adjustment time is 0.0162460803985596 s ( 50.67 )
2024-06-10 00:07:32.177064 INFO::Formatting Data.
2024-06-10 00:07:32.178036 INFO::Replacing NaNs with NAs.
2024-06-10 00:07:32.179113 INFO::Removing potential empty rows and columns
2024-06-10 00:07:32.180168 INFO::Found 0 missing values.
2024-06-10 00:07:32.182152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:07:32.182851 INFO::Done
2024-06-10 00:07:32.183593 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:07:32.185624 INFO::Starting hierarchical adjustment
2024-06-10 00:07:32.186489 INFO::Found 2 batches.
2024-06-10 00:07:32.187185 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:07:32.188029 INFO::Using default BPPARAM
2024-06-10 00:07:32.188756 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:07:32.189893 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:07:32.219772 INFO::Done
2024-06-10 00:07:32.221003 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:07:32.223897 INFO::ASW Batch was 0.130482072395433 prior to batch effect correction and is now -0.162378760936159 .
2024-06-10 00:07:32.225259 INFO::Total function execution time is 0.0482211112976074 s and adjustment time is 0.0333480834960938 s ( 69.16 )
2024-06-10 00:07:32.246507 INFO::Formatting Data.
2024-06-10 00:07:32.247838 INFO::Replacing NaNs with NAs.
2024-06-10 00:07:32.249396 INFO::Removing potential empty rows and columns
2024-06-10 00:07:32.251046 INFO::Found 0 missing values.
2024-06-10 00:07:32.252771 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.
2024-06-10 00:07:32.258891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:07:32.259942 INFO::Done
2024-06-10 00:07:32.260948 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:07:32.26513 INFO::Starting hierarchical adjustment
2024-06-10 00:07:32.266375 INFO::Found 2 batches.
2024-06-10 00:07:32.267399 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:07:32.268704 INFO::Using default BPPARAM
2024-06-10 00:07:32.269914 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:07:32.27162 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:07:32.289464 INFO::Done
2024-06-10 00:07:32.29034 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:07:32.293535 INFO::ASW Batch was 0.494837096129397 prior to batch effect correction and is now 0.202286517406879 .
2024-06-10 00:07:32.294311 INFO::ASW Label was 0.650861311808287 prior to batch effect correction and is now 0.757065553032555 .
2024-06-10 00:07:32.295264 INFO::Total function execution time is 0.0489227771759033 s and adjustment time is 0.0232751369476318 s ( 47.58 )
2024-06-10 00:07:32.29622 INFO::Formatting Data.
2024-06-10 00:07:32.297008 INFO::Replacing NaNs with NAs.
2024-06-10 00:07:32.29806 INFO::Removing potential empty rows and columns
2024-06-10 00:07:32.299173 INFO::Found 0 missing values.
2024-06-10 00:07:32.300242 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.
2024-06-10 00:07:32.304219 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:07:32.304973 INFO::Done
2024-06-10 00:07:32.305677 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:07:32.308651 INFO::Starting hierarchical adjustment
2024-06-10 00:07:32.309525 INFO::Found 2 batches.
2024-06-10 00:07:32.310247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:07:32.311034 INFO::Using default BPPARAM
2024-06-10 00:07:32.311746 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:07:32.312834 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:07:32.326597 INFO::Done
2024-06-10 00:07:32.327419 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:07:32.330374 INFO::ASW Batch was 0.494837096129397 prior to batch effect correction and is now 0.202286517406879 .
2024-06-10 00:07:32.331153 INFO::ASW Label was 0.650861311808287 prior to batch effect correction and is now 0.757065553032555 .
2024-06-10 00:07:32.332101 INFO::Total function execution time is 0.0358881950378418 s and adjustment time is 0.0171911716461182 s ( 47.9 )
2024-06-10 00:07:32.589202 INFO::Formatting Data.
2024-06-10 00:07:32.590433 INFO::Replacing NaNs with NAs.
2024-06-10 00:07:32.591884 INFO::Removing potential empty rows and columns
2024-06-10 00:07:32.593939 INFO::Found 0 missing values.
2024-06-10 00:07:32.597877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:07:32.5988 INFO::Done
2024-06-10 00:07:32.59961 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:07:32.60211 INFO::Starting hierarchical adjustment
2024-06-10 00:07:32.603093 INFO::Found 3 batches.
2024-06-10 00:07:32.603887 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:07:32.604775 INFO::Using default BPPARAM
2024-06-10 00:07:32.605666 INFO::Processing subtree level 1
2024-06-10 00:07:45.89895 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:07:45.90109 INFO::Done
2024-06-10 00:07:45.902346 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:07:45.905336 INFO::ASW Batch was -0.125250623267353 prior to batch effect correction and is now -0.125250623267353 .
2024-06-10 00:07:45.906801 INFO::Total function execution time is 13.3176770210266 s and adjustment time is 13.2981090545654 s ( 99.85 )
2024-06-10 00:07:45.90845 INFO::Formatting Data.
2024-06-10 00:07:45.909642 INFO::Typecasting input to dataframe.
2024-06-10 00:07:45.910962 INFO::Replacing NaNs with NAs.
2024-06-10 00:07:45.912449 INFO::Removing potential empty rows and columns
2024-06-10 00:07:45.914043 INFO::Found 0 missing values.
2024-06-10 00:07:45.917997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:07:45.919104 INFO::Done
2024-06-10 00:07:45.920199 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:07:45.922794 INFO::Starting hierarchical adjustment
2024-06-10 00:07:45.923968 INFO::Found 3 batches.
2024-06-10 00:07:45.924944 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:07:45.92601 INFO::Using default BPPARAM
2024-06-10 00:07:45.926992 INFO::Processing subtree level 1
2024-06-10 00:07:59.14646 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:07:59.148615 INFO::Done
2024-06-10 00:07:59.149898 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:07:59.15289 INFO::ASW Batch was -0.125250623267353 prior to batch effect correction and is now -0.125250623267353 .
2024-06-10 00:07:59.1544 INFO::Total function execution time is 13.2459690570831 s and adjustment time is 13.2247829437256 s ( 99.84 )
2024-06-10 00:07:59.17565 INFO::Formatting Data.
2024-06-10 00:07:59.177086 INFO::Typecasting input to dataframe.
2024-06-10 00:07:59.178638 INFO::Replacing NaNs with NAs.
2024-06-10 00:07:59.180291 INFO::Removing potential empty rows and columns
2024-06-10 00:07:59.181964 INFO::Found 0 missing values.
2024-06-10 00:07:59.185827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:07:59.18696 INFO::Done
2024-06-10 00:07:59.188115 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:07:59.191136 INFO::Starting hierarchical adjustment
2024-06-10 00:07:59.192467 INFO::Found 3 batches.
2024-06-10 00:07:59.193601 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:07:59.194823 INFO::Using default BPPARAM
2024-06-10 00:07:59.195952 INFO::Processing subtree level 1
2024-06-10 00:08:12.132341 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:08:12.134519 INFO::Done
2024-06-10 00:08:12.135787 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:08:12.1389 INFO::ASW Batch was -0.0189315624391822 prior to batch effect correction and is now -0.0189315624391822 .
2024-06-10 00:08:12.140376 INFO::Total function execution time is 12.9648149013519 s and adjustment time is 12.9421968460083 s ( 99.83 )
2024-06-10 00:08:24.994662 INFO::Formatting Data.
2024-06-10 00:08:24.99565 INFO::Replacing NaNs with NAs.
2024-06-10 00:08:24.996902 INFO::Removing potential empty rows and columns
2024-06-10 00:08:25.000252 INFO::Found 1000 missing values.
2024-06-10 00:08:25.021143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:08:25.022411 INFO::Done
2024-06-10 00:08:25.023527 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:08:25.032562 INFO::Starting hierarchical adjustment
2024-06-10 00:08:25.033938 INFO::Found 10 batches.
2024-06-10 00:08:25.034993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:08:25.036095 INFO::Using default BPPARAM
2024-06-10 00:08:25.037107 INFO::Processing subtree level 1
2024-06-10 00:08:38.691417 INFO::Processing subtree level 2
2024-06-10 00:08:51.575971 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:08:51.578375 INFO::Done
2024-06-10 00:08:51.579628 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:08:51.588103 INFO::ASW Batch was 0.528494273428276 prior to batch effect correction and is now 0.528494273428276 .
2024-06-10 00:08:51.589309 INFO::ASW Label was 0.31843688488095 prior to batch effect correction and is now 0.31843688488095 .
2024-06-10 00:08:51.590832 INFO::Total function execution time is 26.5962100028992 s and adjustment time is 26.5446429252625 s ( 99.81 )
2024-06-10 00:08:51.592201 INFO::Formatting Data.
2024-06-10 00:08:51.593382 INFO::Replacing NaNs with NAs.
2024-06-10 00:08:51.595156 INFO::Removing potential empty rows and columns
2024-06-10 00:08:51.598359 INFO::Found 1000 missing values.
2024-06-10 00:08:51.616641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:08:51.618024 INFO::Done
2024-06-10 00:08:51.619286 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:08:51.628665 INFO::Starting hierarchical adjustment
2024-06-10 00:08:51.630222 INFO::Found 10 batches.
2024-06-10 00:08:52.313361 INFO::Set up parallel execution backend with 2 workers
2024-06-10 00:08:52.314356 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-10 00:09:00.987101 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:09:00.989382 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:09:01.013509 INFO::Done
2024-06-10 00:09:01.014945 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:09:01.024316 INFO::ASW Batch was 0.528494273428276 prior to batch effect correction and is now 0.528494273428276 .
2024-06-10 00:09:01.025703 INFO::ASW Label was 0.31843688488095 prior to batch effect correction and is now 0.31843688488095 .
2024-06-10 00:09:01.027297 INFO::Total function execution time is 9.43508815765381 s and adjustment time is 9.38345098495483 s ( 99.45 )
2024-06-10 00:09:16.000923 INFO::Formatting Data.
2024-06-10 00:09:16.002312 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:16.003894 INFO::Removing potential empty rows and columns
2024-06-10 00:09:16.005586 INFO::Found 0 missing values.
2024-06-10 00:09:16.010511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:16.011631 INFO::Done
2024-06-10 00:09:16.012683 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:09:16.016596 INFO::Starting hierarchical adjustment
2024-06-10 00:09:16.017857 INFO::Found 3 batches.
2024-06-10 00:09:16.018725 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:09:16.019583 INFO::Using default BPPARAM
2024-06-10 00:09:16.020329 INFO::Processing subtree level 1
2024-06-10 00:09:29.450583 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:09:29.452715 INFO::Done
2024-06-10 00:09:29.453885 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:09:29.457921 INFO::ASW Batch was 0.146008748388627 prior to batch effect correction and is now -0.17716890542385 .
2024-06-10 00:09:29.459028 INFO::ASW Label was -0.151933477581453 prior to batch effect correction and is now -0.0216087494767789 .
2024-06-10 00:09:29.460384 INFO::Total function execution time is 13.4595880508423 s and adjustment time is 13.4350249767303 s ( 99.82 )
2024-06-10 00:09:29.679824 INFO::Formatting Data.
2024-06-10 00:09:29.681406 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:29.683125 INFO::Removing potential empty rows and columns
2024-06-10 00:09:29.68489 INFO::Found 2 missing values.
2024-06-10 00:09:29.688978 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:29.690008 INFO::Done
2024-06-10 00:09:29.742644 INFO::Found NA in Reference column
2024-06-10 00:09:29.760768 INFO::Require at least two references per batch.
2024-06-10 00:09:29.790981 INFO::Formatting Data.
2024-06-10 00:09:29.792338 INFO::Recognized SummarizedExperiment
2024-06-10 00:09:29.793406 INFO::Typecasting input to dataframe.
2024-06-10 00:09:29.804743 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:29.806561 INFO::Removing potential empty rows and columns
2024-06-10 00:09:29.810932 INFO::Found 0 missing values.
2024-06-10 00:09:29.81917 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:29.820321 INFO::Done
2024-06-10 00:09:29.841173 INFO::Formatting Data.
2024-06-10 00:09:29.842491 INFO::Recognized SummarizedExperiment
2024-06-10 00:09:29.843595 INFO::Typecasting input to dataframe.
2024-06-10 00:09:29.863316 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:29.864695 INFO::Removing potential empty rows and columns
2024-06-10 00:09:29.867489 INFO::Found 0 missing values.
2024-06-10 00:09:29.877763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:29.878952 INFO::Done
2024-06-10 00:09:29.900104 INFO::Formatting Data.
2024-06-10 00:09:29.901645 INFO::Recognized SummarizedExperiment
2024-06-10 00:09:29.90275 INFO::Typecasting input to dataframe.
2024-06-10 00:09:29.924161 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:29.925854 INFO::Removing potential empty rows and columns
2024-06-10 00:09:29.927597 INFO::Found 0 missing values.
2024-06-10 00:09:29.929178 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.
2024-06-10 00:09:29.934703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:29.935749 INFO::Done
2024-06-10 00:09:29.952057 INFO::Formatting Data.
2024-06-10 00:09:29.95306 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:29.954137 INFO::Removing potential empty rows and columns
2024-06-10 00:09:29.955253 INFO::Found 0 missing values.
2024-06-10 00:09:29.957875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:29.958582 INFO::Done
2024-06-10 00:09:29.973331 INFO::Formatting Data.
2024-06-10 00:09:29.974301 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:29.975345 INFO::Removing potential empty rows and columns
2024-06-10 00:09:29.976471 INFO::Found 0 missing values.
2024-06-10 00:09:29.979324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:29.980044 INFO::Done
2024-06-10 00:09:30.018528 INFO::Formatting Data.
2024-06-10 00:09:30.019519 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:30.020679 INFO::Removing potential empty rows and columns
2024-06-10 00:09:30.021888 INFO::Found 1 missing values.
2024-06-10 00:09:30.024231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:30.024958 INFO::Done
2024-06-10 00:09:30.049703 INFO::Formatting Data.
2024-06-10 00:09:30.050706 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:30.05175 INFO::Removing potential empty rows and columns
2024-06-10 00:09:30.052833 INFO::Found 2 missing values.
2024-06-10 00:09:30.053989 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.
2024-06-10 00:09:30.056296 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:30.057036 INFO::Done
2024-06-10 00:09:30.072147 INFO::Formatting Data.
2024-06-10 00:09:30.073184 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:30.074323 INFO::Removing potential empty rows and columns
2024-06-10 00:09:30.075439 INFO::Found 2 missing values.
2024-06-10 00:09:30.077221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:30.078038 INFO::Done
2024-06-10 00:09:30.092488 INFO::Formatting Data.
2024-06-10 00:09:30.093471 INFO::Typecasting input to dataframe.
2024-06-10 00:09:30.094533 INFO::Replacing NaNs with NAs.
2024-06-10 00:09:30.095562 INFO::Removing potential empty rows and columns
2024-06-10 00:09:30.096675 INFO::Found 0 missing values.
2024-06-10 00:09:30.099248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:09:30.099957 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
27.23 11.34 260.07
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.86 | 5.42 | 30.98 | |
| compute_asw | 0.00 | 0.02 | 0.01 | |
| count_existing | 0.01 | 0.00 | 0.01 | |
| generate_data_covariables | 0.02 | 0.00 | 0.02 | |
| generate_dataset | 0.02 | 0.00 | 0.01 | |