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 12:07 -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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.2.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2024-11-20 05:27:44 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 05:30:47 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 183.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 30.713 1.295 22.036
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2024-11-20 05:30:33.01842 INFO::Formatting Data.
2024-11-20 05:30:33.020113 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:33.036296 INFO::Removing potential empty rows and columns
2024-11-20 05:30:33.452319 INFO::Found 0 missing values.
2024-11-20 05:30:33.456584 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:33.45733 INFO::Done
2024-11-20 05:30:33.457993 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:33.471866 INFO::Starting hierarchical adjustment
2024-11-20 05:30:33.472867 INFO::Found 3 batches.
2024-11-20 05:30:33.473544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:33.474893 INFO::Using default BPPARAM
2024-11-20 05:30:33.475613 INFO::Processing subtree level 1
2024-11-20 05:30:33.595859 INFO::Adjusting the last 1 batches sequentially
2024-11-20 05:30:33.598042 INFO::Done
2024-11-20 05:30:33.598808 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:33.602122 INFO::ASW Batch was -0.054313075684915 prior to batch effect correction and is now -0.054313075684915 .
2024-11-20 05:30:33.603575 INFO::Total function execution time is 0.585902452468872 s and adjustment time is 0.125380516052246 s ( 21.4 )
2024-11-20 05:30:33.6208 INFO::Formatting Data.
2024-11-20 05:30:33.621702 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:33.622786 INFO::Removing potential empty rows and columns
2024-11-20 05:30:33.624163 INFO::Found 0 missing values.
2024-11-20 05:30:33.625312 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.
2024-11-20 05:30:33.639336 INFO::Formatting Data.
2024-11-20 05:30:33.640232 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:33.641317 INFO::Removing potential empty rows and columns
2024-11-20 05:30:33.642631 INFO::Found 0 missing values.
2024-11-20 05:30:33.643804 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.
2024-11-20 05:30:33.664328 INFO::Formatting Data.
2024-11-20 05:30:33.665231 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:33.666285 INFO::Removing potential empty rows and columns
2024-11-20 05:30:33.667587 INFO::Found 0 missing values.
2024-11-20 05:30:33.668687 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.
2024-11-20 05:30:33.674467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:33.675219 INFO::Done
2024-11-20 05:30:33.675879 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:33.678463 INFO::Starting hierarchical adjustment
2024-11-20 05:30:33.679381 INFO::Found 2 batches.
2024-11-20 05:30:33.68007 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:33.680875 INFO::Using default BPPARAM
2024-11-20 05:30:33.681588 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:33.68279 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:33.711132 INFO::Done
2024-11-20 05:30:33.711962 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:33.71454 INFO::ASW Batch was 0.0106695529450804 prior to batch effect correction and is now -0.104873036031303 .
2024-11-20 05:30:33.715571 INFO::Total function execution time is 0.0513050556182861 s and adjustment time is 0.0318822860717773 s ( 62.14 )
2024-11-20 05:30:33.719079 INFO::Formatting Data.
2024-11-20 05:30:33.719943 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:33.731693 INFO::Formatting Data.
2024-11-20 05:30:33.7326 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:33.733706 INFO::Removing potential empty rows and columns
2024-11-20 05:30:33.73506 INFO::Found 0 missing values.
2024-11-20 05:30:33.738892 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:33.739591 INFO::Done
2024-11-20 05:30:33.740258 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:33.742945 INFO::Starting hierarchical adjustment
2024-11-20 05:30:33.743904 INFO::Found 2 batches.
2024-11-20 05:30:33.744595 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:33.745409 INFO::Using default BPPARAM
2024-11-20 05:30:33.746079 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:33.747279 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:33.766324 INFO::Done
2024-11-20 05:30:33.767115 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:33.769546 INFO::ASW Batch was -0.0408846682677305 prior to batch effect correction and is now -0.124399152974986 .
2024-11-20 05:30:33.770488 INFO::Total function execution time is 0.0388920307159424 s and adjustment time is 0.0225884914398193 s ( 58.08 )
2024-11-20 05:30:33.771827 INFO::Formatting Data.
2024-11-20 05:30:33.772566 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:33.773648 INFO::Removing potential empty rows and columns
2024-11-20 05:30:33.774924 INFO::Found 0 missing values.
2024-11-20 05:30:33.778636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:33.77933 INFO::Done
2024-11-20 05:30:33.779966 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:33.782501 INFO::Starting hierarchical adjustment
2024-11-20 05:30:33.783405 INFO::Found 2 batches.
2024-11-20 05:30:33.784061 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:33.784806 INFO::Using default BPPARAM
2024-11-20 05:30:33.785468 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:33.786609 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:33.805492 INFO::Done
2024-11-20 05:30:33.806282 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:33.814992 INFO::ASW Batch was -0.0408846682677305 prior to batch effect correction and is now -0.124399152974986 .
2024-11-20 05:30:33.816416 INFO::Total function execution time is 0.0445570945739746 s and adjustment time is 0.0222582817077637 s ( 49.95 )
2024-11-20 05:30:36.606617 INFO::Formatting Data.
2024-11-20 05:30:36.607481 INFO::Recognized SummarizedExperiment
2024-11-20 05:30:36.608113 INFO::Typecasting input to dataframe.
2024-11-20 05:30:36.649214 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:36.650648 INFO::Removing potential empty rows and columns
2024-11-20 05:30:36.655628 INFO::Found 0 missing values.
2024-11-20 05:30:36.664932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:36.665735 INFO::Done
2024-11-20 05:30:36.666387 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:36.670929 INFO::Starting hierarchical adjustment
2024-11-20 05:30:36.671882 INFO::Found 2 batches.
2024-11-20 05:30:36.672576 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:36.674001 INFO::Using default BPPARAM
2024-11-20 05:30:36.674692 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:36.67596 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:36.753229 INFO::Done
2024-11-20 05:30:36.754009 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:36.75847 INFO::ASW Batch was -0.00110385137853995 prior to batch effect correction and is now -0.0911060176206114 .
2024-11-20 05:30:36.759562 INFO::Total function execution time is 0.153340101242065 s and adjustment time is 0.0815262794494629 s ( 53.17 )
2024-11-20 05:30:36.781856 INFO::Formatting Data.
2024-11-20 05:30:36.782686 INFO::Recognized SummarizedExperiment
2024-11-20 05:30:36.783367 INFO::Typecasting input to dataframe.
2024-11-20 05:30:36.795256 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:36.796675 INFO::Removing potential empty rows and columns
2024-11-20 05:30:36.801696 INFO::Found 0 missing values.
2024-11-20 05:30:36.811735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:36.812559 INFO::Done
2024-11-20 05:30:36.813249 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:36.817913 INFO::Starting hierarchical adjustment
2024-11-20 05:30:36.818873 INFO::Found 2 batches.
2024-11-20 05:30:36.819562 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:36.820319 INFO::Using default BPPARAM
2024-11-20 05:30:36.82097 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:36.822237 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:36.855812 INFO::Done
2024-11-20 05:30:36.856598 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:36.861131 INFO::ASW Batch was 0.0157153885706786 prior to batch effect correction and is now 0.0157153885706786 .
2024-11-20 05:30:36.862137 INFO::Total function execution time is 0.0802524089813232 s and adjustment time is 0.0371220111846924 s ( 46.26 )
2024-11-20 05:30:36.884424 INFO::Formatting Data.
2024-11-20 05:30:36.885376 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:36.886449 INFO::Removing potential empty rows and columns
2024-11-20 05:30:36.887745 INFO::Found 0 missing values.
2024-11-20 05:30:36.89159 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:36.892298 INFO::Done
2024-11-20 05:30:36.892937 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:36.895363 INFO::Starting hierarchical adjustment
2024-11-20 05:30:36.896253 INFO::Found 3 batches.
2024-11-20 05:30:36.896911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:36.897671 INFO::Using default BPPARAM
2024-11-20 05:30:36.898314 INFO::Processing subtree level 1
2024-11-20 05:30:37.09753 INFO::Adjusting the last 1 batches sequentially
2024-11-20 05:30:37.099796 INFO::Done
2024-11-20 05:30:37.100569 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:37.103763 INFO::ASW Batch was -0.0871753537403576 prior to batch effect correction and is now -0.1491413422426 .
2024-11-20 05:30:37.105004 INFO::Total function execution time is 0.220571994781494 s and adjustment time is 0.203699588775635 s ( 92.35 )
2024-11-20 05:30:37.1249 INFO::Skipping initial DF formatting
2024-11-20 05:30:37.12581 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:37.13137 INFO::Starting hierarchical adjustment
2024-11-20 05:30:37.132457 INFO::Found 5 batches.
2024-11-20 05:30:37.133224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:37.13409 INFO::Using default BPPARAM
2024-11-20 05:30:37.134838 INFO::Processing subtree level 1
2024-11-20 05:30:37.306493 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:37.308537 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:37.337285 INFO::Done
2024-11-20 05:30:37.338142 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:37.343913 INFO::ASW Batch was 0.531474407710359 prior to batch effect correction and is now 0.531474407710359 .
2024-11-20 05:30:37.344749 INFO::ASW Label was 0.364037991695163 prior to batch effect correction and is now 0.364037991695163 .
2024-11-20 05:30:37.345906 INFO::Total function execution time is 0.221053123474121 s and adjustment time is 0.205032587051392 s ( 92.75 )
2024-11-20 05:30:37.370014 INFO::Formatting Data.
2024-11-20 05:30:37.370956 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:37.372148 INFO::Removing potential empty rows and columns
2024-11-20 05:30:37.373477 INFO::Found 0 missing values.
2024-11-20 05:30:37.379143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:37.37995 INFO::Done
2024-11-20 05:30:37.380673 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:37.38457 INFO::Starting hierarchical adjustment
2024-11-20 05:30:37.385584 INFO::Found 5 batches.
2024-11-20 05:30:37.38631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:37.387187 INFO::Using default BPPARAM
2024-11-20 05:30:37.38792 INFO::Processing subtree level 1
2024-11-20 05:30:37.535295 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:37.537292 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:37.559157 INFO::Done
2024-11-20 05:30:37.560036 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:37.564284 INFO::ASW Batch was 0.459997558075943 prior to batch effect correction and is now 0.0598519686333957 .
2024-11-20 05:30:37.565139 INFO::ASW Label was 0.473500978212868 prior to batch effect correction and is now 0.662263919686923 .
2024-11-20 05:30:37.56623 INFO::Total function execution time is 0.19627046585083 s and adjustment time is 0.173741340637207 s ( 88.52 )
2024-11-20 05:30:37.567325 INFO::Formatting Data.
2024-11-20 05:30:37.5682 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:37.569409 INFO::Removing potential empty rows and columns
2024-11-20 05:30:37.570788 INFO::Found 0 missing values.
2024-11-20 05:30:37.57653 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:37.577359 INFO::Done
2024-11-20 05:30:37.578095 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:37.581993 INFO::Starting hierarchical adjustment
2024-11-20 05:30:37.5831 INFO::Found 5 batches.
2024-11-20 05:30:37.58389 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:37.584742 INFO::Using default BPPARAM
2024-11-20 05:30:37.585515 INFO::Processing subtree level 1
2024-11-20 05:30:37.73024 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:37.732591 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:37.755491 INFO::Done
2024-11-20 05:30:37.756417 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:37.76125 INFO::ASW Batch was 0.459997558075943 prior to batch effect correction and is now 0.0598519686333957 .
2024-11-20 05:30:37.762169 INFO::ASW Label was 0.473500978212868 prior to batch effect correction and is now 0.662263919686923 .
2024-11-20 05:30:37.763316 INFO::Total function execution time is 0.195922136306763 s and adjustment time is 0.172648668289185 s ( 88.12 )
2024-11-20 05:30:37.781897 INFO::Formatting Data.
2024-11-20 05:30:37.782906 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:37.784179 INFO::Removing potential empty rows and columns
2024-11-20 05:30:37.78555 INFO::Found 0 missing values.
2024-11-20 05:30:37.791535 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:37.792402 INFO::Done
2024-11-20 05:30:37.793165 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:37.797391 INFO::Starting hierarchical adjustment
2024-11-20 05:30:37.798501 INFO::Found 5 batches.
2024-11-20 05:30:37.799292 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:37.800151 INFO::Using default BPPARAM
2024-11-20 05:30:37.80092 INFO::Processing subtree level 1
2024-11-20 05:30:37.996097 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:37.998152 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:38.021146 INFO::Done
2024-11-20 05:30:38.022117 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:38.026811 INFO::ASW Batch was 0.306723895768191 prior to batch effect correction and is now -0.0788851461336886 .
2024-11-20 05:30:38.027879 INFO::ASW Label was 0.433261678569774 prior to batch effect correction and is now 0.846560228583076 .
2024-11-20 05:30:38.029258 INFO::Total function execution time is 0.247334480285645 s and adjustment time is 0.222812414169312 s ( 90.09 )
2024-11-20 05:30:38.030653 INFO::Formatting Data.
2024-11-20 05:30:38.031699 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:38.033123 INFO::Removing potential empty rows and columns
2024-11-20 05:30:38.034713 INFO::Found 0 missing values.
2024-11-20 05:30:38.041356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:38.042274 INFO::Done
2024-11-20 05:30:38.043005 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:38.075406 INFO::Starting hierarchical adjustment
2024-11-20 05:30:38.076514 INFO::Found 5 batches.
2024-11-20 05:30:38.077294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:38.078103 INFO::Using default BPPARAM
2024-11-20 05:30:38.078792 INFO::Processing subtree level 1
2024-11-20 05:30:38.247206 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:38.249542 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:38.273993 INFO::Done
2024-11-20 05:30:38.274921 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:38.279971 INFO::ASW Batch was 0.306723895768191 prior to batch effect correction and is now -0.0788851461336886 .
2024-11-20 05:30:38.280902 INFO::ASW Label was 0.433261678569774 prior to batch effect correction and is now 0.846560228583076 .
2024-11-20 05:30:38.282196 INFO::Total function execution time is 0.251542329788208 s and adjustment time is 0.197686910629272 s ( 78.59 )
2024-11-20 05:30:38.302697 INFO::Formatting Data.
2024-11-20 05:30:38.303753 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:38.305042 INFO::Removing potential empty rows and columns
2024-11-20 05:30:38.30657 INFO::Found 0 missing values.
2024-11-20 05:30:38.311055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:38.311908 INFO::Done
2024-11-20 05:30:38.312712 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:38.317238 INFO::Starting hierarchical adjustment
2024-11-20 05:30:38.31831 INFO::Found 2 batches.
2024-11-20 05:30:38.319088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:38.319988 INFO::Using default BPPARAM
2024-11-20 05:30:38.320728 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:38.322113 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:38.344764 INFO::Done
2024-11-20 05:30:38.345713 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:38.350199 INFO::ASW Batch was 0.621363927299296 prior to batch effect correction and is now -0.0253234435949375 .
2024-11-20 05:30:38.35113 INFO::ASW Label was 0.438302494559067 prior to batch effect correction and is now 0.928973709137894 .
2024-11-20 05:30:38.352327 INFO::Total function execution time is 0.0496628284454346 s and adjustment time is 0.0266485214233398 s ( 53.66 )
2024-11-20 05:30:38.353446 INFO::Formatting Data.
2024-11-20 05:30:38.354348 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:38.355672 INFO::Removing potential empty rows and columns
2024-11-20 05:30:38.357237 INFO::Found 0 missing values.
2024-11-20 05:30:38.361423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:38.362296 INFO::Done
2024-11-20 05:30:38.363116 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:38.367634 INFO::Starting hierarchical adjustment
2024-11-20 05:30:38.368773 INFO::Found 2 batches.
2024-11-20 05:30:38.369544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:38.370384 INFO::Using default BPPARAM
2024-11-20 05:30:38.371181 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:38.372567 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:38.394455 INFO::Done
2024-11-20 05:30:38.395376 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:38.399648 INFO::ASW Batch was 0.621363927299296 prior to batch effect correction and is now -0.0253234435949375 .
2024-11-20 05:30:38.400583 INFO::ASW Label was 0.438302494559067 prior to batch effect correction and is now 0.928973709137894 .
2024-11-20 05:30:38.401733 INFO::Total function execution time is 0.0482852458953857 s and adjustment time is 0.0259149074554443 s ( 53.67 )
2024-11-20 05:30:38.418754 INFO::Formatting Data.
2024-11-20 05:30:38.419772 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:38.420986 INFO::Removing potential empty rows and columns
2024-11-20 05:30:38.422333 INFO::Found 0 missing values.
2024-11-20 05:30:38.425637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:38.4265 INFO::Done
2024-11-20 05:30:38.427361 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:38.430105 INFO::Starting hierarchical adjustment
2024-11-20 05:30:38.431265 INFO::Found 2 batches.
2024-11-20 05:30:38.432082 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:38.432972 INFO::Using default BPPARAM
2024-11-20 05:30:38.433771 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:38.435144 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:38.482701 INFO::Done
2024-11-20 05:30:38.483616 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:38.486315 INFO::ASW Batch was 0.0931489336871393 prior to batch effect correction and is now -0.133467933645965 .
2024-11-20 05:30:38.487576 INFO::Total function execution time is 0.068894624710083 s and adjustment time is 0.0516684055328369 s ( 75 )
2024-11-20 05:30:38.505576 INFO::Formatting Data.
2024-11-20 05:30:38.506692 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:38.507981 INFO::Removing potential empty rows and columns
2024-11-20 05:30:38.509484 INFO::Found 0 missing values.
2024-11-20 05:30:38.511212 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.
2024-11-20 05:30:38.518843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:38.519762 INFO::Done
2024-11-20 05:30:38.520501 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:38.524659 INFO::Starting hierarchical adjustment
2024-11-20 05:30:38.525784 INFO::Found 2 batches.
2024-11-20 05:30:38.526533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:38.527508 INFO::Using default BPPARAM
2024-11-20 05:30:38.528291 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:38.529685 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:38.554996 INFO::Done
2024-11-20 05:30:38.556099 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:38.560607 INFO::ASW Batch was 0.565838639269387 prior to batch effect correction and is now 0.0227914871711967 .
2024-11-20 05:30:38.561557 INFO::ASW Label was 0.462254349533617 prior to batch effect correction and is now 0.868089202948787 .
2024-11-20 05:30:38.562675 INFO::Total function execution time is 0.0571529865264893 s and adjustment time is 0.0294139385223389 s ( 51.47 )
2024-11-20 05:30:38.563804 INFO::Formatting Data.
2024-11-20 05:30:38.564724 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:38.566204 INFO::Removing potential empty rows and columns
2024-11-20 05:30:38.567915 INFO::Found 0 missing values.
2024-11-20 05:30:38.569369 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.
2024-11-20 05:30:38.575949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:38.576782 INFO::Done
2024-11-20 05:30:38.577533 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:38.581491 INFO::Starting hierarchical adjustment
2024-11-20 05:30:38.582521 INFO::Found 2 batches.
2024-11-20 05:30:38.583286 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:38.584099 INFO::Using default BPPARAM
2024-11-20 05:30:38.584815 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:38.586128 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:38.60934 INFO::Done
2024-11-20 05:30:38.610196 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:38.614291 INFO::ASW Batch was 0.565838639269387 prior to batch effect correction and is now 0.0227914871711967 .
2024-11-20 05:30:38.615194 INFO::ASW Label was 0.462254349533617 prior to batch effect correction and is now 0.868089202948787 .
2024-11-20 05:30:38.616292 INFO::Total function execution time is 0.0525038242340088 s and adjustment time is 0.0270099639892578 s ( 51.44 )
2024-11-20 05:30:38.932852 INFO::Formatting Data.
2024-11-20 05:30:38.933883 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:38.935082 INFO::Removing potential empty rows and columns
2024-11-20 05:30:38.936504 INFO::Found 0 missing values.
2024-11-20 05:30:38.941435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:38.942295 INFO::Done
2024-11-20 05:30:38.943033 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:38.945905 INFO::Starting hierarchical adjustment
2024-11-20 05:30:38.947004 INFO::Found 3 batches.
2024-11-20 05:30:38.947805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:38.948671 INFO::Using default BPPARAM
2024-11-20 05:30:38.949467 INFO::Processing subtree level 1
2024-11-20 05:30:39.105932 INFO::Adjusting the last 1 batches sequentially
2024-11-20 05:30:39.108298 INFO::Done
2024-11-20 05:30:39.109193 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:39.112712 INFO::ASW Batch was -0.0602839626902604 prior to batch effect correction and is now -0.0602839626902604 .
2024-11-20 05:30:39.114144 INFO::Total function execution time is 0.181271076202393 s and adjustment time is 0.161525249481201 s ( 89.11 )
2024-11-20 05:30:39.115735 INFO::Formatting Data.
2024-11-20 05:30:39.116739 INFO::Typecasting input to dataframe.
2024-11-20 05:30:39.117913 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:39.119313 INFO::Removing potential empty rows and columns
2024-11-20 05:30:39.121003 INFO::Found 0 missing values.
2024-11-20 05:30:39.125942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:39.126866 INFO::Done
2024-11-20 05:30:39.127751 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:39.131056 INFO::Starting hierarchical adjustment
2024-11-20 05:30:39.132249 INFO::Found 3 batches.
2024-11-20 05:30:39.133203 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:39.134274 INFO::Using default BPPARAM
2024-11-20 05:30:39.135261 INFO::Processing subtree level 1
2024-11-20 05:30:39.31092 INFO::Adjusting the last 1 batches sequentially
2024-11-20 05:30:39.313228 INFO::Done
2024-11-20 05:30:39.314081 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:39.317612 INFO::ASW Batch was -0.0602839626902604 prior to batch effect correction and is now -0.0602839626902604 .
2024-11-20 05:30:39.319034 INFO::Total function execution time is 0.203266859054565 s and adjustment time is 0.181233167648315 s ( 89.16 )
2024-11-20 05:30:39.337948 INFO::Formatting Data.
2024-11-20 05:30:39.339009 INFO::Typecasting input to dataframe.
2024-11-20 05:30:39.340203 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:39.341513 INFO::Removing potential empty rows and columns
2024-11-20 05:30:39.34307 INFO::Found 0 missing values.
2024-11-20 05:30:39.347606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:39.348467 INFO::Done
2024-11-20 05:30:39.349236 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:39.352018 INFO::Starting hierarchical adjustment
2024-11-20 05:30:39.353083 INFO::Found 3 batches.
2024-11-20 05:30:39.35386 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:39.354734 INFO::Using default BPPARAM
2024-11-20 05:30:39.355528 INFO::Processing subtree level 1
2024-11-20 05:30:39.543993 INFO::Adjusting the last 1 batches sequentially
2024-11-20 05:30:39.54668 INFO::Done
2024-11-20 05:30:39.547687 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:39.551861 INFO::ASW Batch was -0.147509287065446 prior to batch effect correction and is now -0.147509287065446 .
2024-11-20 05:30:39.553468 INFO::Total function execution time is 0.215501308441162 s and adjustment time is 0.193810939788818 s ( 89.93 )
2024-11-20 05:30:39.767908 INFO::Formatting Data.
2024-11-20 05:30:39.768996 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:39.770618 INFO::Removing potential empty rows and columns
2024-11-20 05:30:39.775475 INFO::Found 1000 missing values.
2024-11-20 05:30:39.806555 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:39.807499 INFO::Done
2024-11-20 05:30:39.808236 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:39.816157 INFO::Starting hierarchical adjustment
2024-11-20 05:30:39.817333 INFO::Found 10 batches.
2024-11-20 05:30:39.818094 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:39.819031 INFO::Using default BPPARAM
2024-11-20 05:30:39.81992 INFO::Processing subtree level 1
2024-11-20 05:30:40.030927 INFO::Processing subtree level 2
2024-11-20 05:30:40.26324 INFO::Adjusting the last 1 batches sequentially
2024-11-20 05:30:40.26576 INFO::Done
2024-11-20 05:30:40.266603 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:40.274982 INFO::ASW Batch was 0.48108528841663 prior to batch effect correction and is now 0.48108528841663 .
2024-11-20 05:30:40.275984 INFO::ASW Label was 0.363930283948784 prior to batch effect correction and is now 0.363930283948784 .
2024-11-20 05:30:40.277302 INFO::Total function execution time is 0.509421348571777 s and adjustment time is 0.448711156845093 s ( 88.08 )
2024-11-20 05:30:40.278519 INFO::Formatting Data.
2024-11-20 05:30:40.283332 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:40.285603 INFO::Removing potential empty rows and columns
2024-11-20 05:30:40.290632 INFO::Found 1000 missing values.
2024-11-20 05:30:40.324011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:40.325145 INFO::Done
2024-11-20 05:30:40.325934 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:40.333979 INFO::Starting hierarchical adjustment
2024-11-20 05:30:40.335219 INFO::Found 10 batches.
2024-11-20 05:30:41.698719 INFO::Set up parallel execution backend with 2 workers
2024-11-20 05:30:41.699805 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-11-20 05:30:43.099777 INFO::Adjusting the last 2 batches sequentially
2024-11-20 05:30:43.101791 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-20 05:30:43.126029 INFO::Done
2024-11-20 05:30:43.126793 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:43.13339 INFO::ASW Batch was 0.48108528841663 prior to batch effect correction and is now 0.48108528841663 .
2024-11-20 05:30:43.134146 INFO::ASW Label was 0.363930283948784 prior to batch effect correction and is now 0.363930283948784 .
2024-11-20 05:30:43.135164 INFO::Total function execution time is 2.85663652420044 s and adjustment time is 2.79108428955078 s ( 97.71 )
2024-11-20 05:30:43.315606 INFO::Formatting Data.
2024-11-20 05:30:43.316609 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:43.317905 INFO::Removing potential empty rows and columns
2024-11-20 05:30:43.31938 INFO::Found 0 missing values.
2024-11-20 05:30:43.324723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:43.325525 INFO::Done
2024-11-20 05:30:43.326229 INFO::Acquiring quality metrics before batch effect correction.
2024-11-20 05:30:43.329957 INFO::Starting hierarchical adjustment
2024-11-20 05:30:43.330923 INFO::Found 3 batches.
2024-11-20 05:30:43.331676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-20 05:30:43.3325 INFO::Using default BPPARAM
2024-11-20 05:30:43.333244 INFO::Processing subtree level 1
2024-11-20 05:30:43.4627 INFO::Adjusting the last 1 batches sequentially
2024-11-20 05:30:43.464913 INFO::Done
2024-11-20 05:30:43.465726 INFO::Acquiring quality metrics after batch effect correction.
2024-11-20 05:30:43.470035 INFO::ASW Batch was 0.284388445117842 prior to batch effect correction and is now -0.17354652919823 .
2024-11-20 05:30:43.470896 INFO::ASW Label was -0.192918734999532 prior to batch effect correction and is now 0.0165664832804604 .
2024-11-20 05:30:43.472187 INFO::Total function execution time is 0.156594038009644 s and adjustment time is 0.134199857711792 s ( 85.7 )
2024-11-20 05:30:43.632909 INFO::Formatting Data.
2024-11-20 05:30:43.633864 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:43.634979 INFO::Removing potential empty rows and columns
2024-11-20 05:30:43.636374 INFO::Found 2 missing values.
2024-11-20 05:30:43.640253 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:43.640932 INFO::Done
2024-11-20 05:30:43.678373 INFO::Found NA in Reference column
2024-11-20 05:30:43.691888 INFO::Require at least two references per batch.
2024-11-20 05:30:43.720634 INFO::Formatting Data.
2024-11-20 05:30:43.721555 INFO::Recognized SummarizedExperiment
2024-11-20 05:30:43.722246 INFO::Typecasting input to dataframe.
2024-11-20 05:30:43.736093 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:43.737616 INFO::Removing potential empty rows and columns
2024-11-20 05:30:43.743202 INFO::Found 0 missing values.
2024-11-20 05:30:43.754014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:43.754874 INFO::Done
2024-11-20 05:30:43.776464 INFO::Formatting Data.
2024-11-20 05:30:43.777426 INFO::Recognized SummarizedExperiment
2024-11-20 05:30:43.778134 INFO::Typecasting input to dataframe.
2024-11-20 05:30:43.808661 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:43.810333 INFO::Removing potential empty rows and columns
2024-11-20 05:30:43.81604 INFO::Found 0 missing values.
2024-11-20 05:30:43.834657 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:43.835558 INFO::Done
2024-11-20 05:30:43.858186 INFO::Formatting Data.
2024-11-20 05:30:43.859166 INFO::Recognized SummarizedExperiment
2024-11-20 05:30:43.85988 INFO::Typecasting input to dataframe.
2024-11-20 05:30:43.885355 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:43.886725 INFO::Removing potential empty rows and columns
2024-11-20 05:30:43.888262 INFO::Found 0 missing values.
2024-11-20 05:30:43.889547 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.
2024-11-20 05:30:43.896308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:43.897188 INFO::Done
2024-11-20 05:30:43.911851 INFO::Formatting Data.
2024-11-20 05:30:43.912849 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:43.914035 INFO::Removing potential empty rows and columns
2024-11-20 05:30:43.915485 INFO::Found 0 missing values.
2024-11-20 05:30:43.92065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:43.921559 INFO::Done
2024-11-20 05:30:43.937621 INFO::Formatting Data.
2024-11-20 05:30:43.93872 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:43.939898 INFO::Removing potential empty rows and columns
2024-11-20 05:30:43.941331 INFO::Found 0 missing values.
2024-11-20 05:30:43.945622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:43.946467 INFO::Done
2024-11-20 05:30:43.987811 INFO::Formatting Data.
2024-11-20 05:30:43.988864 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:43.990535 INFO::Removing potential empty rows and columns
2024-11-20 05:30:43.992216 INFO::Found 1 missing values.
2024-11-20 05:30:43.99637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:43.997159 INFO::Done
2024-11-20 05:30:44.023666 INFO::Formatting Data.
2024-11-20 05:30:44.024649 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:44.025831 INFO::Removing potential empty rows and columns
2024-11-20 05:30:44.027191 INFO::Found 2 missing values.
2024-11-20 05:30:44.028427 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.
2024-11-20 05:30:44.031803 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:44.032554 INFO::Done
2024-11-20 05:30:44.047008 INFO::Formatting Data.
2024-11-20 05:30:44.048066 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:44.049284 INFO::Removing potential empty rows and columns
2024-11-20 05:30:44.050585 INFO::Found 2 missing values.
2024-11-20 05:30:44.052825 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:44.053581 INFO::Done
2024-11-20 05:30:44.06892 INFO::Formatting Data.
2024-11-20 05:30:44.069986 INFO::Typecasting input to dataframe.
2024-11-20 05:30:44.071366 INFO::Replacing NaNs with NAs.
2024-11-20 05:30:44.072588 INFO::Removing potential empty rows and columns
2024-11-20 05:30:44.07408 INFO::Found 0 missing values.
2024-11-20 05:30:44.078467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-20 05:30:44.079289 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.450 4.664 25.527
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 30.713 | 1.295 | 22.036 | |
| compute_asw | 0.035 | 0.000 | 0.034 | |
| count_existing | 0.018 | 0.000 | 0.019 | |
| generate_data_covariables | 0.016 | 0.000 | 0.016 | |
| generate_dataset | 0.016 | 0.000 | 0.016 | |