Yannis Schumann
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.2.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz |
| StartedAt: 2024-11-19 23:17:51 -0500 (Tue, 19 Nov 2024) |
| EndedAt: 2024-11-19 23:19:18 -0500 (Tue, 19 Nov 2024) |
| EllapsedTime: 87.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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 22.448 2.001 17.195
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
2024-11-19 23:18:40.813155 INFO::Formatting Data.
2024-11-19 23:18:40.8143 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:40.823004 INFO::Removing potential empty rows and columns
2024-11-19 23:18:41.051064 INFO::Found 0 missing values.
2024-11-19 23:18:41.05371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:41.054127 INFO::Done
2024-11-19 23:18:41.054505 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:41.063416 INFO::Starting hierarchical adjustment
2024-11-19 23:18:41.063995 INFO::Found 3 batches.
2024-11-19 23:18:41.06441 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:41.065308 INFO::Using default BPPARAM
2024-11-19 23:18:41.065759 INFO::Processing subtree level 1
2024-11-19 23:18:41.16618 INFO::Adjusting the last 1 batches sequentially
2024-11-19 23:18:41.168013 INFO::Done
2024-11-19 23:18:41.168541 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:41.170971 INFO::ASW Batch was -0.0799222999311531 prior to batch effect correction and is now -0.0799222999311531 .
2024-11-19 23:18:41.171916 INFO::Total function execution time is 0.359230041503906 s and adjustment time is 0.104139566421509 s ( 28.99 )
2024-11-19 23:18:41.187723 INFO::Formatting Data.
2024-11-19 23:18:41.188229 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:41.188919 INFO::Removing potential empty rows and columns
2024-11-19 23:18:41.189796 INFO::Found 0 missing values.
2024-11-19 23:18:41.190515 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.
2024-11-19 23:18:41.199141 INFO::Formatting Data.
2024-11-19 23:18:41.199629 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:41.20031 INFO::Removing potential empty rows and columns
2024-11-19 23:18:41.201091 INFO::Found 0 missing values.
2024-11-19 23:18:41.201741 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.
2024-11-19 23:18:41.213755 INFO::Formatting Data.
2024-11-19 23:18:41.214251 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:41.214868 INFO::Removing potential empty rows and columns
2024-11-19 23:18:41.215656 INFO::Found 0 missing values.
2024-11-19 23:18:41.216352 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.
2024-11-19 23:18:41.219835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:41.220279 INFO::Done
2024-11-19 23:18:41.220664 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:41.222404 INFO::Starting hierarchical adjustment
2024-11-19 23:18:41.223055 INFO::Found 2 batches.
2024-11-19 23:18:41.223506 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:41.224053 INFO::Using default BPPARAM
2024-11-19 23:18:41.224508 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:41.225273 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:41.245336 INFO::Done
2024-11-19 23:18:41.245822 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:41.247546 INFO::ASW Batch was 0.0934468100912924 prior to batch effect correction and is now -0.118794916154578 .
2024-11-19 23:18:41.248234 INFO::Total function execution time is 0.0344533920288086 s and adjustment time is 0.022428035736084 s ( 65.1 )
2024-11-19 23:18:41.25049 INFO::Formatting Data.
2024-11-19 23:18:41.251009 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:41.258605 INFO::Formatting Data.
2024-11-19 23:18:41.25921 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:41.25996 INFO::Removing potential empty rows and columns
2024-11-19 23:18:41.260928 INFO::Found 0 missing values.
2024-11-19 23:18:41.263467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:41.263912 INFO::Done
2024-11-19 23:18:41.264417 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:41.266228 INFO::Starting hierarchical adjustment
2024-11-19 23:18:41.266852 INFO::Found 2 batches.
2024-11-19 23:18:41.267327 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:41.267836 INFO::Using default BPPARAM
2024-11-19 23:18:41.268326 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:41.269122 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:41.281971 INFO::Done
2024-11-19 23:18:41.28242 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:41.284004 INFO::ASW Batch was -0.0363947145739074 prior to batch effect correction and is now -0.117339056041756 .
2024-11-19 23:18:41.284612 INFO::Total function execution time is 0.0260100364685059 s and adjustment time is 0.0152246952056885 s ( 58.53 )
2024-11-19 23:18:41.285449 INFO::Formatting Data.
2024-11-19 23:18:41.285919 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:41.286606 INFO::Removing potential empty rows and columns
2024-11-19 23:18:41.287457 INFO::Found 0 missing values.
2024-11-19 23:18:41.289852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:41.290322 INFO::Done
2024-11-19 23:18:41.290733 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:41.292316 INFO::Starting hierarchical adjustment
2024-11-19 23:18:41.292894 INFO::Found 2 batches.
2024-11-19 23:18:41.293336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:41.293794 INFO::Using default BPPARAM
2024-11-19 23:18:41.294232 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:41.294982 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:41.307599 INFO::Done
2024-11-19 23:18:41.308075 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:41.30975 INFO::ASW Batch was -0.0363947145739074 prior to batch effect correction and is now -0.117339056041756 .
2024-11-19 23:18:41.310377 INFO::Total function execution time is 0.0249190330505371 s and adjustment time is 0.0148293972015381 s ( 59.51 )
2024-11-19 23:18:43.223487 INFO::Formatting Data.
2024-11-19 23:18:43.224068 INFO::Recognized SummarizedExperiment
2024-11-19 23:18:43.224382 INFO::Typecasting input to dataframe.
2024-11-19 23:18:43.246505 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:43.247261 INFO::Removing potential empty rows and columns
2024-11-19 23:18:43.249726 INFO::Found 0 missing values.
2024-11-19 23:18:43.254287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:43.254638 INFO::Done
2024-11-19 23:18:43.254975 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:43.25737 INFO::Starting hierarchical adjustment
2024-11-19 23:18:43.257835 INFO::Found 2 batches.
2024-11-19 23:18:43.258206 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:43.258866 INFO::Using default BPPARAM
2024-11-19 23:18:43.259226 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:43.259824 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:43.296561 INFO::Done
2024-11-19 23:18:43.297046 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:43.299405 INFO::ASW Batch was -0.0127353637389781 prior to batch effect correction and is now -0.08947307301859 .
2024-11-19 23:18:43.299962 INFO::Total function execution time is 0.0767190456390381 s and adjustment time is 0.038806676864624 s ( 50.58 )
2024-11-19 23:18:43.312774 INFO::Formatting Data.
2024-11-19 23:18:43.313191 INFO::Recognized SummarizedExperiment
2024-11-19 23:18:43.313511 INFO::Typecasting input to dataframe.
2024-11-19 23:18:43.319449 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:43.320139 INFO::Removing potential empty rows and columns
2024-11-19 23:18:43.322476 INFO::Found 0 missing values.
2024-11-19 23:18:43.326998 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:43.327353 INFO::Done
2024-11-19 23:18:43.327693 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:43.329963 INFO::Starting hierarchical adjustment
2024-11-19 23:18:43.330435 INFO::Found 2 batches.
2024-11-19 23:18:43.330767 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:43.331163 INFO::Using default BPPARAM
2024-11-19 23:18:43.331497 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:43.332102 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:43.348102 INFO::Done
2024-11-19 23:18:43.348465 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:43.35064 INFO::ASW Batch was -0.00105768075991233 prior to batch effect correction and is now -0.00105768075991233 .
2024-11-19 23:18:43.351207 INFO::Total function execution time is 0.038395881652832 s and adjustment time is 0.0177762508392334 s ( 46.3 )
2024-11-19 23:18:43.363305 INFO::Formatting Data.
2024-11-19 23:18:43.36378 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:43.364367 INFO::Removing potential empty rows and columns
2024-11-19 23:18:43.365038 INFO::Found 0 missing values.
2024-11-19 23:18:43.366826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:43.367195 INFO::Done
2024-11-19 23:18:43.367517 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:43.36877 INFO::Starting hierarchical adjustment
2024-11-19 23:18:43.369293 INFO::Found 3 batches.
2024-11-19 23:18:43.369628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:43.370027 INFO::Using default BPPARAM
2024-11-19 23:18:43.370347 INFO::Processing subtree level 1
2024-11-19 23:18:43.51023 INFO::Adjusting the last 1 batches sequentially
2024-11-19 23:18:43.512086 INFO::Done
2024-11-19 23:18:43.512632 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:43.518996 INFO::ASW Batch was -0.054170323466007 prior to batch effect correction and is now -0.149891278697364 .
2024-11-19 23:18:43.519826 INFO::Total function execution time is 0.156444311141968 s and adjustment time is 0.142852306365967 s ( 91.31 )
2024-11-19 23:18:43.547889 INFO::Skipping initial DF formatting
2024-11-19 23:18:43.55136 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:43.554615 INFO::Starting hierarchical adjustment
2024-11-19 23:18:43.555258 INFO::Found 5 batches.
2024-11-19 23:18:43.555728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:43.556243 INFO::Using default BPPARAM
2024-11-19 23:18:43.556673 INFO::Processing subtree level 1
2024-11-19 23:18:43.734314 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:43.73586 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:43.773018 INFO::Done
2024-11-19 23:18:43.773643 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:43.77707 INFO::ASW Batch was 0.50639866234612 prior to batch effect correction and is now 0.50639866234612 .
2024-11-19 23:18:43.777514 INFO::ASW Label was 0.37437181338258 prior to batch effect correction and is now 0.37437181338258 .
2024-11-19 23:18:43.778212 INFO::Total function execution time is 0.230412244796753 s and adjustment time is 0.217861413955688 s ( 94.55 )
2024-11-19 23:18:43.792643 INFO::Formatting Data.
2024-11-19 23:18:43.793166 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:43.79383 INFO::Removing potential empty rows and columns
2024-11-19 23:18:43.794618 INFO::Found 0 missing values.
2024-11-19 23:18:43.797702 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:43.798141 INFO::Done
2024-11-19 23:18:43.79852 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:43.800656 INFO::Starting hierarchical adjustment
2024-11-19 23:18:43.801249 INFO::Found 5 batches.
2024-11-19 23:18:43.801641 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:43.802131 INFO::Using default BPPARAM
2024-11-19 23:18:43.802525 INFO::Processing subtree level 1
2024-11-19 23:18:43.968441 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:43.97411 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:43.996302 INFO::Done
2024-11-19 23:18:43.996978 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:43.999579 INFO::ASW Batch was 0.39098029409066 prior to batch effect correction and is now -0.0636067393049084 .
2024-11-19 23:18:44.000058 INFO::ASW Label was 0.312935756283023 prior to batch effect correction and is now 0.78523256351721 .
2024-11-19 23:18:44.000682 INFO::Total function execution time is 0.208041906356812 s and adjustment time is 0.195140361785889 s ( 93.8 )
2024-11-19 23:18:44.001356 INFO::Formatting Data.
2024-11-19 23:18:44.001824 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:44.002517 INFO::Removing potential empty rows and columns
2024-11-19 23:18:44.003302 INFO::Found 0 missing values.
2024-11-19 23:18:44.006416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:44.006878 INFO::Done
2024-11-19 23:18:44.007372 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:44.009522 INFO::Starting hierarchical adjustment
2024-11-19 23:18:44.010088 INFO::Found 5 batches.
2024-11-19 23:18:44.01049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:44.011012 INFO::Using default BPPARAM
2024-11-19 23:18:44.011447 INFO::Processing subtree level 1
2024-11-19 23:18:44.176306 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:44.181956 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:44.207487 INFO::Done
2024-11-19 23:18:44.207927 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:44.210483 INFO::ASW Batch was 0.39098029409066 prior to batch effect correction and is now -0.0636067393049084 .
2024-11-19 23:18:44.210917 INFO::ASW Label was 0.312935756283023 prior to batch effect correction and is now 0.78523256351721 .
2024-11-19 23:18:44.21157 INFO::Total function execution time is 0.210193872451782 s and adjustment time is 0.197532176971436 s ( 93.98 )
2024-11-19 23:18:44.223096 INFO::Formatting Data.
2024-11-19 23:18:44.223625 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:44.224364 INFO::Removing potential empty rows and columns
2024-11-19 23:18:44.225168 INFO::Found 0 missing values.
2024-11-19 23:18:44.228417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:44.228837 INFO::Done
2024-11-19 23:18:44.229244 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:44.231414 INFO::Starting hierarchical adjustment
2024-11-19 23:18:44.232003 INFO::Found 5 batches.
2024-11-19 23:18:44.232407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:44.232907 INFO::Using default BPPARAM
2024-11-19 23:18:44.233328 INFO::Processing subtree level 1
2024-11-19 23:18:44.47385 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:44.479468 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:44.504221 INFO::Done
2024-11-19 23:18:44.50472 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:44.511327 INFO::ASW Batch was 0.304456044302889 prior to batch effect correction and is now -0.0697726084941993 .
2024-11-19 23:18:44.51182 INFO::ASW Label was 0.393179190676491 prior to batch effect correction and is now 0.795887509236104 .
2024-11-19 23:18:44.516716 INFO::Total function execution time is 0.293470859527588 s and adjustment time is 0.272348880767822 s ( 92.8 )
2024-11-19 23:18:44.51761 INFO::Formatting Data.
2024-11-19 23:18:44.518144 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:44.519031 INFO::Removing potential empty rows and columns
2024-11-19 23:18:44.519908 INFO::Found 0 missing values.
2024-11-19 23:18:44.546293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:44.546791 INFO::Done
2024-11-19 23:18:44.547218 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:44.549978 INFO::Starting hierarchical adjustment
2024-11-19 23:18:44.550565 INFO::Found 5 batches.
2024-11-19 23:18:44.551001 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:44.551504 INFO::Using default BPPARAM
2024-11-19 23:18:44.551935 INFO::Processing subtree level 1
2024-11-19 23:18:44.745215 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:44.747046 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:44.773871 INFO::Done
2024-11-19 23:18:44.774607 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:44.777742 INFO::ASW Batch was 0.304456044302889 prior to batch effect correction and is now -0.0697726084941993 .
2024-11-19 23:18:44.77824 INFO::ASW Label was 0.393179190676491 prior to batch effect correction and is now 0.795887509236104 .
2024-11-19 23:18:44.77893 INFO::Total function execution time is 0.261291027069092 s and adjustment time is 0.223392724990845 s ( 85.5 )
2024-11-19 23:18:44.792286 INFO::Formatting Data.
2024-11-19 23:18:44.792864 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:44.793655 INFO::Removing potential empty rows and columns
2024-11-19 23:18:44.794614 INFO::Found 0 missing values.
2024-11-19 23:18:44.797079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:44.797513 INFO::Done
2024-11-19 23:18:44.797923 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:44.800545 INFO::Starting hierarchical adjustment
2024-11-19 23:18:44.801166 INFO::Found 2 batches.
2024-11-19 23:18:44.801596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:44.80214 INFO::Using default BPPARAM
2024-11-19 23:18:44.802548 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:44.803269 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:44.81591 INFO::Done
2024-11-19 23:18:44.816403 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:44.818921 INFO::ASW Batch was 0.465110223024693 prior to batch effect correction and is now -0.0111706739526396 .
2024-11-19 23:18:44.819416 INFO::ASW Label was 0.569628618571894 prior to batch effect correction and is now 0.862664311538163 .
2024-11-19 23:18:44.820075 INFO::Total function execution time is 0.0277957916259766 s and adjustment time is 0.0149116516113281 s ( 53.65 )
2024-11-19 23:18:44.820698 INFO::Formatting Data.
2024-11-19 23:18:44.821205 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:44.82192 INFO::Removing potential empty rows and columns
2024-11-19 23:18:44.822828 INFO::Found 0 missing values.
2024-11-19 23:18:44.8252 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:44.825632 INFO::Done
2024-11-19 23:18:44.826073 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:44.828481 INFO::Starting hierarchical adjustment
2024-11-19 23:18:44.829078 INFO::Found 2 batches.
2024-11-19 23:18:44.829519 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:44.830024 INFO::Using default BPPARAM
2024-11-19 23:18:44.83043 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:44.831178 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:44.842904 INFO::Done
2024-11-19 23:18:44.843378 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:44.845707 INFO::ASW Batch was 0.465110223024693 prior to batch effect correction and is now -0.0111706739526396 .
2024-11-19 23:18:44.846182 INFO::ASW Label was 0.569628618571894 prior to batch effect correction and is now 0.862664311538163 .
2024-11-19 23:18:44.846725 INFO::Total function execution time is 0.0260417461395264 s and adjustment time is 0.013986349105835 s ( 53.71 )
2024-11-19 23:18:44.856771 INFO::Formatting Data.
2024-11-19 23:18:44.857326 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:44.858145 INFO::Removing potential empty rows and columns
2024-11-19 23:18:44.858857 INFO::Found 0 missing values.
2024-11-19 23:18:44.860621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:44.861077 INFO::Done
2024-11-19 23:18:44.861479 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:44.862903 INFO::Starting hierarchical adjustment
2024-11-19 23:18:44.863501 INFO::Found 2 batches.
2024-11-19 23:18:44.863918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:44.864411 INFO::Using default BPPARAM
2024-11-19 23:18:44.86483 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:44.865552 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:44.892506 INFO::Done
2024-11-19 23:18:44.892975 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:44.89456 INFO::ASW Batch was -0.0472081931393709 prior to batch effect correction and is now -0.107556992290305 .
2024-11-19 23:18:44.895155 INFO::Total function execution time is 0.0384087562561035 s and adjustment time is 0.0291557312011719 s ( 75.91 )
2024-11-19 23:18:44.905034 INFO::Formatting Data.
2024-11-19 23:18:44.905563 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:44.906232 INFO::Removing potential empty rows and columns
2024-11-19 23:18:44.907048 INFO::Found 0 missing values.
2024-11-19 23:18:44.908037 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.
2024-11-19 23:18:44.9119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:44.912374 INFO::Done
2024-11-19 23:18:44.912797 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:44.915253 INFO::Starting hierarchical adjustment
2024-11-19 23:18:44.915885 INFO::Found 2 batches.
2024-11-19 23:18:44.916364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:44.916909 INFO::Using default BPPARAM
2024-11-19 23:18:44.917347 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:44.918181 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:44.932529 INFO::Done
2024-11-19 23:18:44.933021 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:44.935656 INFO::ASW Batch was 0.595824031565136 prior to batch effect correction and is now -0.0356633817929427 .
2024-11-19 23:18:44.936206 INFO::ASW Label was 0.444486002019265 prior to batch effect correction and is now 0.923868050038731 .
2024-11-19 23:18:44.936844 INFO::Total function execution time is 0.0318517684936523 s and adjustment time is 0.0167598724365234 s ( 52.62 )
2024-11-19 23:18:44.93744 INFO::Formatting Data.
2024-11-19 23:18:44.937881 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:44.93856 INFO::Removing potential empty rows and columns
2024-11-19 23:18:44.939323 INFO::Found 0 missing values.
2024-11-19 23:18:44.940037 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.
2024-11-19 23:18:44.943574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:44.944014 INFO::Done
2024-11-19 23:18:44.944407 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:44.946508 INFO::Starting hierarchical adjustment
2024-11-19 23:18:44.94706 INFO::Found 2 batches.
2024-11-19 23:18:44.947478 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:44.947909 INFO::Using default BPPARAM
2024-11-19 23:18:44.948314 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:44.949009 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:44.961627 INFO::Done
2024-11-19 23:18:44.962072 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:44.964207 INFO::ASW Batch was 0.595824031565136 prior to batch effect correction and is now -0.0356633817929427 .
2024-11-19 23:18:44.964636 INFO::ASW Label was 0.444486002019265 prior to batch effect correction and is now 0.923868050038731 .
2024-11-19 23:18:44.965216 INFO::Total function execution time is 0.0277817249298096 s and adjustment time is 0.0147027969360352 s ( 52.92 )
2024-11-19 23:18:45.125092 INFO::Formatting Data.
2024-11-19 23:18:45.125623 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:45.126271 INFO::Removing potential empty rows and columns
2024-11-19 23:18:45.127098 INFO::Found 0 missing values.
2024-11-19 23:18:45.129498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:45.129888 INFO::Done
2024-11-19 23:18:45.130293 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:45.131828 INFO::Starting hierarchical adjustment
2024-11-19 23:18:45.132377 INFO::Found 3 batches.
2024-11-19 23:18:45.132784 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:45.13328 INFO::Using default BPPARAM
2024-11-19 23:18:45.133675 INFO::Processing subtree level 1
2024-11-19 23:18:45.267071 INFO::Adjusting the last 1 batches sequentially
2024-11-19 23:18:45.268869 INFO::Done
2024-11-19 23:18:45.269426 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:45.271759 INFO::ASW Batch was -0.0543834878603596 prior to batch effect correction and is now -0.0543834878603596 .
2024-11-19 23:18:45.272599 INFO::Total function execution time is 0.147512197494507 s and adjustment time is 0.136568784713745 s ( 92.58 )
2024-11-19 23:18:45.27354 INFO::Formatting Data.
2024-11-19 23:18:45.278118 INFO::Typecasting input to dataframe.
2024-11-19 23:18:45.278759 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:45.279534 INFO::Removing potential empty rows and columns
2024-11-19 23:18:45.280467 INFO::Found 0 missing values.
2024-11-19 23:18:45.28701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:45.287482 INFO::Done
2024-11-19 23:18:45.287908 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:45.293655 INFO::Starting hierarchical adjustment
2024-11-19 23:18:45.294252 INFO::Found 3 batches.
2024-11-19 23:18:45.29469 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:45.29907 INFO::Using default BPPARAM
2024-11-19 23:18:45.299547 INFO::Processing subtree level 1
2024-11-19 23:18:45.428229 INFO::Adjusting the last 1 batches sequentially
2024-11-19 23:18:45.429993 INFO::Done
2024-11-19 23:18:45.430535 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:45.436863 INFO::ASW Batch was -0.0543834878603596 prior to batch effect correction and is now -0.0543834878603596 .
2024-11-19 23:18:45.437678 INFO::Total function execution time is 0.164110422134399 s and adjustment time is 0.135814189910889 s ( 82.76 )
2024-11-19 23:18:45.460897 INFO::Formatting Data.
2024-11-19 23:18:45.461459 INFO::Typecasting input to dataframe.
2024-11-19 23:18:45.462121 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:45.462821 INFO::Removing potential empty rows and columns
2024-11-19 23:18:45.463753 INFO::Found 0 missing values.
2024-11-19 23:18:45.486023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:45.486767 INFO::Done
2024-11-19 23:18:45.487227 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:45.489173 INFO::Starting hierarchical adjustment
2024-11-19 23:18:45.489798 INFO::Found 3 batches.
2024-11-19 23:18:45.490249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:45.490734 INFO::Using default BPPARAM
2024-11-19 23:18:45.491173 INFO::Processing subtree level 1
2024-11-19 23:18:45.59899 INFO::Adjusting the last 1 batches sequentially
2024-11-19 23:18:45.600773 INFO::Done
2024-11-19 23:18:45.60129 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:45.60378 INFO::ASW Batch was -0.0669965443575895 prior to batch effect correction and is now -0.0669965443575895 .
2024-11-19 23:18:45.604672 INFO::Total function execution time is 0.143735885620117 s and adjustment time is 0.111102342605591 s ( 77.3 )
2024-11-19 23:18:46.340189 INFO::Formatting Data.
2024-11-19 23:18:46.34073 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:46.341689 INFO::Removing potential empty rows and columns
2024-11-19 23:18:46.344358 INFO::Found 1000 missing values.
2024-11-19 23:18:46.361457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:46.362011 INFO::Done
2024-11-19 23:18:46.362432 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:46.366584 INFO::Starting hierarchical adjustment
2024-11-19 23:18:46.367189 INFO::Found 10 batches.
2024-11-19 23:18:46.367599 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:46.368106 INFO::Using default BPPARAM
2024-11-19 23:18:46.368518 INFO::Processing subtree level 1
2024-11-19 23:18:46.623224 INFO::Processing subtree level 2
2024-11-19 23:18:46.807954 INFO::Adjusting the last 1 batches sequentially
2024-11-19 23:18:46.809887 INFO::Done
2024-11-19 23:18:46.814552 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:46.824208 INFO::ASW Batch was 0.464810286143952 prior to batch effect correction and is now 0.464810286143952 .
2024-11-19 23:18:46.824762 INFO::ASW Label was 0.375353137782713 prior to batch effect correction and is now 0.375353137782713 .
2024-11-19 23:18:46.828659 INFO::Total function execution time is 0.488451242446899 s and adjustment time is 0.442802667617798 s ( 90.65 )
2024-11-19 23:18:46.82945 INFO::Formatting Data.
2024-11-19 23:18:46.830063 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:46.835481 INFO::Removing potential empty rows and columns
2024-11-19 23:18:46.838265 INFO::Found 1000 missing values.
2024-11-19 23:18:46.865796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:46.866313 INFO::Done
2024-11-19 23:18:46.866752 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:46.87131 INFO::Starting hierarchical adjustment
2024-11-19 23:18:46.871995 INFO::Found 10 batches.
2024-11-19 23:18:47.83755 INFO::Set up parallel execution backend with 2 workers
2024-11-19 23:18:47.839336 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-11-19 23:18:48.972949 INFO::Adjusting the last 2 batches sequentially
2024-11-19 23:18:48.974521 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-19 23:18:48.987246 INFO::Done
2024-11-19 23:18:48.987684 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:48.991331 INFO::ASW Batch was 0.464810286143952 prior to batch effect correction and is now 0.464810286143952 .
2024-11-19 23:18:48.991727 INFO::ASW Label was 0.375353137782713 prior to batch effect correction and is now 0.375353137782713 .
2024-11-19 23:18:48.992279 INFO::Total function execution time is 2.16286277770996 s and adjustment time is 2.11543130874634 s ( 97.81 )
2024-11-19 23:18:49.138727 INFO::Formatting Data.
2024-11-19 23:18:49.139292 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:49.140019 INFO::Removing potential empty rows and columns
2024-11-19 23:18:49.140888 INFO::Found 0 missing values.
2024-11-19 23:18:49.144103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:49.14451 INFO::Done
2024-11-19 23:18:49.144904 INFO::Acquiring quality metrics before batch effect correction.
2024-11-19 23:18:49.147009 INFO::Starting hierarchical adjustment
2024-11-19 23:18:49.147571 INFO::Found 3 batches.
2024-11-19 23:18:49.147983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-19 23:18:49.148454 INFO::Using default BPPARAM
2024-11-19 23:18:49.148845 INFO::Processing subtree level 1
2024-11-19 23:18:50.05504 INFO::Adjusting the last 1 batches sequentially
2024-11-19 23:18:50.056847 INFO::Done
2024-11-19 23:18:50.057414 INFO::Acquiring quality metrics after batch effect correction.
2024-11-19 23:18:50.060342 INFO::ASW Batch was 0.128534867559238 prior to batch effect correction and is now -0.133684238168349 .
2024-11-19 23:18:50.060841 INFO::ASW Label was -0.164700451846607 prior to batch effect correction and is now -0.0568781412236702 .
2024-11-19 23:18:50.061683 INFO::Total function execution time is 0.922934293746948 s and adjustment time is 0.909408807754517 s ( 98.53 )
2024-11-19 23:18:50.158864 INFO::Formatting Data.
2024-11-19 23:18:50.159427 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:50.160125 INFO::Removing potential empty rows and columns
2024-11-19 23:18:50.160985 INFO::Found 2 missing values.
2024-11-19 23:18:50.163242 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:50.163682 INFO::Done
2024-11-19 23:18:50.185183 INFO::Found NA in Reference column
2024-11-19 23:18:50.193018 INFO::Require at least two references per batch.
2024-11-19 23:18:50.210411 INFO::Formatting Data.
2024-11-19 23:18:50.210868 INFO::Recognized SummarizedExperiment
2024-11-19 23:18:50.211289 INFO::Typecasting input to dataframe.
2024-11-19 23:18:50.219667 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:50.220476 INFO::Removing potential empty rows and columns
2024-11-19 23:18:50.223519 INFO::Found 0 missing values.
2024-11-19 23:18:50.229401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:50.229851 INFO::Done
2024-11-19 23:18:50.24188 INFO::Formatting Data.
2024-11-19 23:18:50.242355 INFO::Recognized SummarizedExperiment
2024-11-19 23:18:50.242743 INFO::Typecasting input to dataframe.
2024-11-19 23:18:50.256801 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:50.257635 INFO::Removing potential empty rows and columns
2024-11-19 23:18:50.260599 INFO::Found 0 missing values.
2024-11-19 23:18:50.270461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:50.270927 INFO::Done
2024-11-19 23:18:50.283238 INFO::Formatting Data.
2024-11-19 23:18:50.283756 INFO::Recognized SummarizedExperiment
2024-11-19 23:18:50.284195 INFO::Typecasting input to dataframe.
2024-11-19 23:18:50.297764 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:50.29847 INFO::Removing potential empty rows and columns
2024-11-19 23:18:50.29932 INFO::Found 0 missing values.
2024-11-19 23:18:50.300051 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.
2024-11-19 23:18:50.304108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:50.304542 INFO::Done
2024-11-19 23:18:50.312632 INFO::Formatting Data.
2024-11-19 23:18:50.313147 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:50.313857 INFO::Removing potential empty rows and columns
2024-11-19 23:18:50.315209 INFO::Found 0 missing values.
2024-11-19 23:18:50.317809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:50.318251 INFO::Done
2024-11-19 23:18:50.327672 INFO::Formatting Data.
2024-11-19 23:18:50.328179 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:50.328798 INFO::Removing potential empty rows and columns
2024-11-19 23:18:50.329564 INFO::Found 0 missing values.
2024-11-19 23:18:50.331852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:50.332292 INFO::Done
2024-11-19 23:18:50.355425 INFO::Formatting Data.
2024-11-19 23:18:50.355931 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:50.356793 INFO::Removing potential empty rows and columns
2024-11-19 23:18:50.35781 INFO::Found 1 missing values.
2024-11-19 23:18:50.359834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:50.360249 INFO::Done
2024-11-19 23:18:50.374979 INFO::Formatting Data.
2024-11-19 23:18:50.375498 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:50.376158 INFO::Removing potential empty rows and columns
2024-11-19 23:18:50.376855 INFO::Found 2 missing values.
2024-11-19 23:18:50.377583 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.
2024-11-19 23:18:50.37942 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:50.379859 INFO::Done
2024-11-19 23:18:50.388038 INFO::Formatting Data.
2024-11-19 23:18:50.388533 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:50.389218 INFO::Removing potential empty rows and columns
2024-11-19 23:18:50.389981 INFO::Found 2 missing values.
2024-11-19 23:18:50.391315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:50.391733 INFO::Done
2024-11-19 23:18:50.400623 INFO::Formatting Data.
2024-11-19 23:18:50.401138 INFO::Typecasting input to dataframe.
2024-11-19 23:18:50.401809 INFO::Replacing NaNs with NAs.
2024-11-19 23:18:50.402455 INFO::Removing potential empty rows and columns
2024-11-19 23:18:50.403259 INFO::Found 0 missing values.
2024-11-19 23:18:50.405643 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-19 23:18:50.406112 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
15.405 4.109 20.023
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 22.448 | 2.001 | 17.195 | |
| compute_asw | 0.016 | 0.000 | 0.016 | |
| count_existing | 0.010 | 0.000 | 0.009 | |
| generate_data_covariables | 0.006 | 0.002 | 0.008 | |
| generate_dataset | 0.007 | 0.000 | 0.008 | |