Yannis Schumann
| Snapshot Date: 2024-11-07 13:40 -0500 (Thu, 07 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 2024-11-08 12:06 -0500 (Fri, 08 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4765 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2024-11-07 19:47:18 -0500 (Thu, 07 Nov 2024) |
| EndedAt: 2024-11-07 19:52:02 -0500 (Thu, 07 Nov 2024) |
| EllapsedTime: 284.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 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 19.657 1.014 14.061
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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: x86_64-apple-darwin20
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")
2024-11-07 19:51:46.558559 INFO::Formatting Data.
2024-11-07 19:51:46.56298 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:46.572906 INFO::Removing potential empty rows and columns
2024-11-07 19:51:46.787895 INFO::Found 0 missing values.
2024-11-07 19:51:46.790585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:46.791141 INFO::Done
2024-11-07 19:51:46.791598 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:46.803122 INFO::Starting hierarchical adjustment
2024-11-07 19:51:46.803921 INFO::Found 3 batches.
2024-11-07 19:51:46.804424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:46.805412 INFO::Using default BPPARAM
2024-11-07 19:51:46.80587 INFO::Processing subtree level 1
2024-11-07 19:51:46.90296 INFO::Adjusting the last 1 batches sequentially
2024-11-07 19:51:46.905902 INFO::Done
2024-11-07 19:51:46.907117 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:46.912606 INFO::ASW Batch was -0.0529893387681615 prior to batch effect correction and is now -0.0529893387681615 .
2024-11-07 19:51:46.9143 INFO::Total function execution time is 0.356443881988525 s and adjustment time is 0.102150201797485 s ( 28.66 )
2024-11-07 19:51:46.934828 INFO::Formatting Data.
2024-11-07 19:51:46.935549 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:46.936361 INFO::Removing potential empty rows and columns
2024-11-07 19:51:46.93727 INFO::Found 0 missing values.
2024-11-07 19:51:46.938078 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.
2024-11-07 19:51:46.947166 INFO::Formatting Data.
2024-11-07 19:51:46.947819 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:46.948561 INFO::Removing potential empty rows and columns
2024-11-07 19:51:46.949428 INFO::Found 0 missing values.
2024-11-07 19:51:46.950181 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.
2024-11-07 19:51:46.96669 INFO::Formatting Data.
2024-11-07 19:51:46.967331 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:46.968069 INFO::Removing potential empty rows and columns
2024-11-07 19:51:46.968901 INFO::Found 0 missing values.
2024-11-07 19:51:46.969728 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.
2024-11-07 19:51:46.973489 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:46.973927 INFO::Done
2024-11-07 19:51:46.974362 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:46.976005 INFO::Starting hierarchical adjustment
2024-11-07 19:51:46.976569 INFO::Found 2 batches.
2024-11-07 19:51:46.976992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:46.977537 INFO::Using default BPPARAM
2024-11-07 19:51:46.977963 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:46.978714 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:46.998793 INFO::Done
2024-11-07 19:51:46.999395 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:47.00111 INFO::ASW Batch was -0.0300876483816937 prior to batch effect correction and is now -0.0976178123643544 .
2024-11-07 19:51:47.001768 INFO::Total function execution time is 0.0351579189300537 s and adjustment time is 0.022305965423584 s ( 63.45 )
2024-11-07 19:51:47.004219 INFO::Formatting Data.
2024-11-07 19:51:47.004728 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:47.011813 INFO::Formatting Data.
2024-11-07 19:51:47.012354 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:47.013074 INFO::Removing potential empty rows and columns
2024-11-07 19:51:47.013948 INFO::Found 0 missing values.
2024-11-07 19:51:47.01625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:47.016677 INFO::Done
2024-11-07 19:51:47.01711 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:47.018727 INFO::Starting hierarchical adjustment
2024-11-07 19:51:47.019295 INFO::Found 2 batches.
2024-11-07 19:51:47.019721 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:47.020206 INFO::Using default BPPARAM
2024-11-07 19:51:47.020637 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:47.021474 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:47.033411 INFO::Done
2024-11-07 19:51:47.03396 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:47.03554 INFO::ASW Batch was 0.0578631071413021 prior to batch effect correction and is now -0.105291601981111 .
2024-11-07 19:51:47.036191 INFO::Total function execution time is 0.0243990421295166 s and adjustment time is 0.0142240524291992 s ( 58.3 )
2024-11-07 19:51:47.037038 INFO::Formatting Data.
2024-11-07 19:51:47.037554 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:47.03827 INFO::Removing potential empty rows and columns
2024-11-07 19:51:47.039115 INFO::Found 0 missing values.
2024-11-07 19:51:47.041472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:47.041909 INFO::Done
2024-11-07 19:51:47.042341 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:47.04402 INFO::Starting hierarchical adjustment
2024-11-07 19:51:47.044604 INFO::Found 2 batches.
2024-11-07 19:51:47.045048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:47.045545 INFO::Using default BPPARAM
2024-11-07 19:51:47.045999 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:47.046744 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:47.059094 INFO::Done
2024-11-07 19:51:47.059659 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:47.061301 INFO::ASW Batch was 0.0578631071413021 prior to batch effect correction and is now -0.105291601981111 .
2024-11-07 19:51:47.061957 INFO::Total function execution time is 0.0249221324920654 s and adjustment time is 0.0145881175994873 s ( 58.53 )
2024-11-07 19:51:49.539961 INFO::Formatting Data.
2024-11-07 19:51:49.540554 INFO::Recognized SummarizedExperiment
2024-11-07 19:51:49.540975 INFO::Typecasting input to dataframe.
2024-11-07 19:51:49.565253 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:49.566201 INFO::Removing potential empty rows and columns
2024-11-07 19:51:49.568631 INFO::Found 0 missing values.
2024-11-07 19:51:49.573327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:49.573769 INFO::Done
2024-11-07 19:51:49.574162 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:49.576799 INFO::Starting hierarchical adjustment
2024-11-07 19:51:49.577331 INFO::Found 2 batches.
2024-11-07 19:51:49.577713 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:49.578531 INFO::Using default BPPARAM
2024-11-07 19:51:49.578937 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:49.57971 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:49.61847 INFO::Done
2024-11-07 19:51:49.619048 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:49.621966 INFO::ASW Batch was 0.0180637716783309 prior to batch effect correction and is now -0.0932726354531505 .
2024-11-07 19:51:49.62264 INFO::Total function execution time is 0.0829188823699951 s and adjustment time is 0.041208028793335 s ( 49.7 )
2024-11-07 19:51:49.638159 INFO::Formatting Data.
2024-11-07 19:51:49.638747 INFO::Recognized SummarizedExperiment
2024-11-07 19:51:49.639164 INFO::Typecasting input to dataframe.
2024-11-07 19:51:49.647157 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:49.648175 INFO::Removing potential empty rows and columns
2024-11-07 19:51:49.651229 INFO::Found 0 missing values.
2024-11-07 19:51:49.6573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:49.657859 INFO::Done
2024-11-07 19:51:49.658327 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:49.661454 INFO::Starting hierarchical adjustment
2024-11-07 19:51:49.662059 INFO::Found 2 batches.
2024-11-07 19:51:49.662496 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:49.662984 INFO::Using default BPPARAM
2024-11-07 19:51:49.663408 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:49.664257 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:49.684893 INFO::Done
2024-11-07 19:51:49.685475 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:49.688517 INFO::ASW Batch was -0.0276419650889543 prior to batch effect correction and is now -0.0276419650889543 .
2024-11-07 19:51:49.689217 INFO::Total function execution time is 0.0510470867156982 s and adjustment time is 0.0229110717773438 s ( 44.88 )
2024-11-07 19:51:49.707288 INFO::Formatting Data.
2024-11-07 19:51:49.707963 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:49.708769 INFO::Removing potential empty rows and columns
2024-11-07 19:51:49.709583 INFO::Found 0 missing values.
2024-11-07 19:51:49.711897 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:49.71232 INFO::Done
2024-11-07 19:51:49.712735 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:49.714317 INFO::Starting hierarchical adjustment
2024-11-07 19:51:49.714874 INFO::Found 3 batches.
2024-11-07 19:51:49.715287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:49.715766 INFO::Using default BPPARAM
2024-11-07 19:51:49.716179 INFO::Processing subtree level 1
2024-11-07 19:51:49.845668 INFO::Adjusting the last 1 batches sequentially
2024-11-07 19:51:49.849863 INFO::Done
2024-11-07 19:51:49.851053 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:49.860348 INFO::ASW Batch was -0.0928082002992615 prior to batch effect correction and is now -0.164293787609877 .
2024-11-07 19:51:49.86272 INFO::Total function execution time is 0.15510106086731 s and adjustment time is 0.135056972503662 s ( 87.08 )
2024-11-07 19:51:49.881761 INFO::Skipping initial DF formatting
2024-11-07 19:51:49.882409 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:49.886886 INFO::Starting hierarchical adjustment
2024-11-07 19:51:49.887632 INFO::Found 5 batches.
2024-11-07 19:51:49.888131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:49.888698 INFO::Using default BPPARAM
2024-11-07 19:51:49.889195 INFO::Processing subtree level 1
2024-11-07 19:51:50.004066 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:50.009111 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:50.030532 INFO::Done
2024-11-07 19:51:50.031313 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:50.039314 INFO::ASW Batch was 0.549703545598183 prior to batch effect correction and is now 0.549703545598183 .
2024-11-07 19:51:50.039983 INFO::ASW Label was 0.36066079227031 prior to batch effect correction and is now 0.36066079227031 .
2024-11-07 19:51:50.042408 INFO::Total function execution time is 0.159892082214355 s and adjustment time is 0.143028974533081 s ( 89.45 )
2024-11-07 19:51:50.06392 INFO::Formatting Data.
2024-11-07 19:51:50.064692 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:50.06587 INFO::Removing potential empty rows and columns
2024-11-07 19:51:50.066803 INFO::Found 0 missing values.
2024-11-07 19:51:50.070412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:50.070907 INFO::Done
2024-11-07 19:51:50.071359 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:50.07406 INFO::Starting hierarchical adjustment
2024-11-07 19:51:50.075166 INFO::Found 5 batches.
2024-11-07 19:51:50.075608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:50.076151 INFO::Using default BPPARAM
2024-11-07 19:51:50.076605 INFO::Processing subtree level 1
2024-11-07 19:51:50.174968 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:50.180865 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:50.20548 INFO::Done
2024-11-07 19:51:50.206308 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:50.210941 INFO::ASW Batch was 0.352740363846789 prior to batch effect correction and is now -0.0248052571175467 .
2024-11-07 19:51:50.212274 INFO::ASW Label was 0.340812404940443 prior to batch effect correction and is now 0.821620019990603 .
2024-11-07 19:51:50.213925 INFO::Total function execution time is 0.150090932846069 s and adjustment time is 0.130393981933594 s ( 86.88 )
2024-11-07 19:51:50.214722 INFO::Formatting Data.
2024-11-07 19:51:50.215267 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:50.216433 INFO::Removing potential empty rows and columns
2024-11-07 19:51:50.217614 INFO::Found 0 missing values.
2024-11-07 19:51:50.221324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:50.22217 INFO::Done
2024-11-07 19:51:50.222612 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:50.225488 INFO::Starting hierarchical adjustment
2024-11-07 19:51:50.226277 INFO::Found 5 batches.
2024-11-07 19:51:50.226744 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:50.227269 INFO::Using default BPPARAM
2024-11-07 19:51:50.227714 INFO::Processing subtree level 1
2024-11-07 19:51:50.327854 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:50.333966 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:50.359746 INFO::Done
2024-11-07 19:51:50.361051 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:50.365185 INFO::ASW Batch was 0.352740363846789 prior to batch effect correction and is now -0.0248052571175467 .
2024-11-07 19:51:50.366167 INFO::ASW Label was 0.340812404940443 prior to batch effect correction and is now 0.821620019990603 .
2024-11-07 19:51:50.367689 INFO::Total function execution time is 0.152952909469604 s and adjustment time is 0.133722066879272 s ( 87.43 )
2024-11-07 19:51:50.386486 INFO::Formatting Data.
2024-11-07 19:51:50.387182 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:50.388346 INFO::Removing potential empty rows and columns
2024-11-07 19:51:50.389266 INFO::Found 0 missing values.
2024-11-07 19:51:50.392738 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:50.393235 INFO::Done
2024-11-07 19:51:50.394039 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:50.396642 INFO::Starting hierarchical adjustment
2024-11-07 19:51:50.397284 INFO::Found 5 batches.
2024-11-07 19:51:50.398115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:50.399151 INFO::Using default BPPARAM
2024-11-07 19:51:50.39959 INFO::Processing subtree level 1
2024-11-07 19:51:50.501632 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:50.508397 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:50.532477 INFO::Done
2024-11-07 19:51:50.533214 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:50.537417 INFO::ASW Batch was 0.565938378893556 prior to batch effect correction and is now -0.0269083695177937 .
2024-11-07 19:51:50.538002 INFO::ASW Label was 0.216881701797062 prior to batch effect correction and is now 0.80802428682428 .
2024-11-07 19:51:50.539501 INFO::Total function execution time is 0.153055906295776 s and adjustment time is 0.135273933410645 s ( 88.38 )
2024-11-07 19:51:50.540353 INFO::Formatting Data.
2024-11-07 19:51:50.540904 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:50.542419 INFO::Removing potential empty rows and columns
2024-11-07 19:51:50.543673 INFO::Found 0 missing values.
2024-11-07 19:51:50.547081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:50.54752 INFO::Done
2024-11-07 19:51:50.547944 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:50.550628 INFO::Starting hierarchical adjustment
2024-11-07 19:51:50.551243 INFO::Found 5 batches.
2024-11-07 19:51:50.551716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:50.552219 INFO::Using default BPPARAM
2024-11-07 19:51:50.553288 INFO::Processing subtree level 1
2024-11-07 19:51:50.649928 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:50.65499 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:50.679538 INFO::Done
2024-11-07 19:51:50.680314 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:50.684533 INFO::ASW Batch was 0.565938378893556 prior to batch effect correction and is now -0.0269083695177937 .
2024-11-07 19:51:50.704581 INFO::ASW Label was 0.216881701797062 prior to batch effect correction and is now 0.80802428682428 .
2024-11-07 19:51:50.706296 INFO::Total function execution time is 0.165891885757446 s and adjustment time is 0.128394842147827 s ( 77.4 )
2024-11-07 19:51:50.730637 INFO::Formatting Data.
2024-11-07 19:51:50.731342 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:50.732435 INFO::Removing potential empty rows and columns
2024-11-07 19:51:50.733365 INFO::Found 0 missing values.
2024-11-07 19:51:50.735488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:50.735904 INFO::Done
2024-11-07 19:51:50.736328 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:50.738859 INFO::Starting hierarchical adjustment
2024-11-07 19:51:50.739464 INFO::Found 2 batches.
2024-11-07 19:51:50.739913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:50.740438 INFO::Using default BPPARAM
2024-11-07 19:51:50.740861 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:50.74157 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:50.753761 INFO::Done
2024-11-07 19:51:50.754347 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:50.756857 INFO::ASW Batch was 0.724969308461688 prior to batch effect correction and is now 0.0247268011640957 .
2024-11-07 19:51:50.757707 INFO::ASW Label was 0.339414105237849 prior to batch effect correction and is now 0.879076487360704 .
2024-11-07 19:51:50.758428 INFO::Total function execution time is 0.027864933013916 s and adjustment time is 0.0144128799438477 s ( 51.72 )
2024-11-07 19:51:50.759115 INFO::Formatting Data.
2024-11-07 19:51:50.759635 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:50.760368 INFO::Removing potential empty rows and columns
2024-11-07 19:51:50.761232 INFO::Found 0 missing values.
2024-11-07 19:51:50.76348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:50.763929 INFO::Done
2024-11-07 19:51:50.764391 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:50.76688 INFO::Starting hierarchical adjustment
2024-11-07 19:51:50.767492 INFO::Found 2 batches.
2024-11-07 19:51:50.767939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:50.768439 INFO::Using default BPPARAM
2024-11-07 19:51:50.769273 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:50.770058 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:50.782004 INFO::Done
2024-11-07 19:51:50.782578 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:50.785036 INFO::ASW Batch was 0.724969308461688 prior to batch effect correction and is now 0.0247268011640957 .
2024-11-07 19:51:50.78554 INFO::ASW Label was 0.339414105237849 prior to batch effect correction and is now 0.879076487360704 .
2024-11-07 19:51:50.786347 INFO::Total function execution time is 0.027108907699585 s and adjustment time is 0.0146090984344482 s ( 53.89 )
2024-11-07 19:51:50.799461 INFO::Formatting Data.
2024-11-07 19:51:50.800165 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:50.800944 INFO::Removing potential empty rows and columns
2024-11-07 19:51:50.801705 INFO::Found 0 missing values.
2024-11-07 19:51:50.803461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:50.803909 INFO::Done
2024-11-07 19:51:50.804346 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:50.80642 INFO::Starting hierarchical adjustment
2024-11-07 19:51:50.807046 INFO::Found 2 batches.
2024-11-07 19:51:50.807544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:50.808087 INFO::Using default BPPARAM
2024-11-07 19:51:50.808553 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:50.809312 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:50.836299 INFO::Done
2024-11-07 19:51:50.83722 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:50.839371 INFO::ASW Batch was 0.443341515369906 prior to batch effect correction and is now -0.0663941003256707 .
2024-11-07 19:51:50.840048 INFO::Total function execution time is 0.0406661033630371 s and adjustment time is 0.0293478965759277 s ( 72.17 )
2024-11-07 19:51:50.854271 INFO::Formatting Data.
2024-11-07 19:51:50.855005 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:50.855766 INFO::Removing potential empty rows and columns
2024-11-07 19:51:50.856626 INFO::Found 0 missing values.
2024-11-07 19:51:50.857646 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.
2024-11-07 19:51:50.861637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:50.862118 INFO::Done
2024-11-07 19:51:50.862559 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:50.865126 INFO::Starting hierarchical adjustment
2024-11-07 19:51:50.865721 INFO::Found 2 batches.
2024-11-07 19:51:50.866166 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:50.866674 INFO::Using default BPPARAM
2024-11-07 19:51:50.867117 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:50.867932 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:50.881746 INFO::Done
2024-11-07 19:51:50.882347 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:50.884715 INFO::ASW Batch was 0.241312851687976 prior to batch effect correction and is now -0.0364837813917129 .
2024-11-07 19:51:50.885205 INFO::ASW Label was 0.801318250064734 prior to batch effect correction and is now 0.958078840820492 .
2024-11-07 19:51:50.885884 INFO::Total function execution time is 0.0317091941833496 s and adjustment time is 0.0161368846893311 s ( 50.89 )
2024-11-07 19:51:50.886544 INFO::Formatting Data.
2024-11-07 19:51:50.887125 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:50.888056 INFO::Removing potential empty rows and columns
2024-11-07 19:51:50.888877 INFO::Found 0 missing values.
2024-11-07 19:51:50.889667 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.
2024-11-07 19:51:50.893439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:50.893938 INFO::Done
2024-11-07 19:51:50.894361 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:50.896871 INFO::Starting hierarchical adjustment
2024-11-07 19:51:50.897476 INFO::Found 2 batches.
2024-11-07 19:51:50.898048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:50.898614 INFO::Using default BPPARAM
2024-11-07 19:51:50.899077 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:50.899893 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:50.913983 INFO::Done
2024-11-07 19:51:50.914575 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:50.917116 INFO::ASW Batch was 0.241312851687976 prior to batch effect correction and is now -0.0364837813917129 .
2024-11-07 19:51:50.917614 INFO::ASW Label was 0.801318250064734 prior to batch effect correction and is now 0.958078840820492 .
2024-11-07 19:51:50.918294 INFO::Total function execution time is 0.0317630767822266 s and adjustment time is 0.016618013381958 s ( 52.32 )
2024-11-07 19:51:51.102732 INFO::Formatting Data.
2024-11-07 19:51:51.103466 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:51.104281 INFO::Removing potential empty rows and columns
2024-11-07 19:51:51.105132 INFO::Found 0 missing values.
2024-11-07 19:51:51.107684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:51.108156 INFO::Done
2024-11-07 19:51:51.108601 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:51.110399 INFO::Starting hierarchical adjustment
2024-11-07 19:51:51.111006 INFO::Found 3 batches.
2024-11-07 19:51:51.111418 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:51.111928 INFO::Using default BPPARAM
2024-11-07 19:51:51.112379 INFO::Processing subtree level 1
2024-11-07 19:51:51.197311 INFO::Adjusting the last 1 batches sequentially
2024-11-07 19:51:51.202296 INFO::Done
2024-11-07 19:51:51.204202 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:51.212377 INFO::ASW Batch was -0.00998895512387027 prior to batch effect correction and is now -0.00998895512387027 .
2024-11-07 19:51:51.214827 INFO::Total function execution time is 0.112044095993042 s and adjustment time is 0.0913870334625244 s ( 81.56 )
2024-11-07 19:51:51.216883 INFO::Formatting Data.
2024-11-07 19:51:51.217493 INFO::Typecasting input to dataframe.
2024-11-07 19:51:51.218478 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:51.220229 INFO::Removing potential empty rows and columns
2024-11-07 19:51:51.221178 INFO::Found 0 missing values.
2024-11-07 19:51:51.223603 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:51.224044 INFO::Done
2024-11-07 19:51:51.22449 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:51.226478 INFO::Starting hierarchical adjustment
2024-11-07 19:51:51.227073 INFO::Found 3 batches.
2024-11-07 19:51:51.227859 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:51.228387 INFO::Using default BPPARAM
2024-11-07 19:51:51.229121 INFO::Processing subtree level 1
2024-11-07 19:51:51.44207 INFO::Adjusting the last 1 batches sequentially
2024-11-07 19:51:51.444708 INFO::Done
2024-11-07 19:51:51.445378 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:51.4488 INFO::ASW Batch was -0.00998895512387027 prior to batch effect correction and is now -0.00998895512387027 .
2024-11-07 19:51:51.469055 INFO::Total function execution time is 0.251468896865845 s and adjustment time is 0.217738151550293 s ( 86.59 )
2024-11-07 19:51:51.496864 INFO::Formatting Data.
2024-11-07 19:51:51.497589 INFO::Typecasting input to dataframe.
2024-11-07 19:51:51.498956 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:51.500493 INFO::Removing potential empty rows and columns
2024-11-07 19:51:51.503476 INFO::Found 0 missing values.
2024-11-07 19:51:51.506474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:51.507298 INFO::Done
2024-11-07 19:51:51.50816 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:51.50994 INFO::Starting hierarchical adjustment
2024-11-07 19:51:51.510551 INFO::Found 3 batches.
2024-11-07 19:51:51.511286 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:51.512691 INFO::Using default BPPARAM
2024-11-07 19:51:51.513185 INFO::Processing subtree level 1
2024-11-07 19:51:51.738033 INFO::Adjusting the last 1 batches sequentially
2024-11-07 19:51:51.740801 INFO::Done
2024-11-07 19:51:51.741574 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:51.744934 INFO::ASW Batch was -0.04316557320043 prior to batch effect correction and is now -0.04316557320043 .
2024-11-07 19:51:51.75711 INFO::Total function execution time is 0.259732007980347 s and adjustment time is 0.23033595085144 s ( 88.68 )
2024-11-07 19:51:52.054078 INFO::Formatting Data.
2024-11-07 19:51:52.054826 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:52.055862 INFO::Removing potential empty rows and columns
2024-11-07 19:51:52.05824 INFO::Found 1000 missing values.
2024-11-07 19:51:52.075744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:52.076462 INFO::Done
2024-11-07 19:51:52.076968 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:52.08185 INFO::Starting hierarchical adjustment
2024-11-07 19:51:52.082558 INFO::Found 10 batches.
2024-11-07 19:51:52.083046 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:52.083635 INFO::Using default BPPARAM
2024-11-07 19:51:52.084102 INFO::Processing subtree level 1
2024-11-07 19:51:52.231396 INFO::Processing subtree level 2
2024-11-07 19:51:52.426967 INFO::Adjusting the last 1 batches sequentially
2024-11-07 19:51:52.434969 INFO::Done
2024-11-07 19:51:52.436484 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:52.44593 INFO::ASW Batch was 0.467559324241701 prior to batch effect correction and is now 0.467559324241701 .
2024-11-07 19:51:52.447236 INFO::ASW Label was 0.346971940863632 prior to batch effect correction and is now 0.346971940863632 .
2024-11-07 19:51:52.450099 INFO::Total function execution time is 0.395106077194214 s and adjustment time is 0.352529048919678 s ( 89.22 )
2024-11-07 19:51:52.451328 INFO::Formatting Data.
2024-11-07 19:51:52.45268 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:52.454016 INFO::Removing potential empty rows and columns
2024-11-07 19:51:52.456599 INFO::Found 1000 missing values.
2024-11-07 19:51:52.47854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:52.479204 INFO::Done
2024-11-07 19:51:52.479724 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:52.484646 INFO::Starting hierarchical adjustment
2024-11-07 19:51:52.485722 INFO::Found 10 batches.
2024-11-07 19:51:53.319787 INFO::Set up parallel execution backend with 2 workers
2024-11-07 19:51:53.3204 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-11-07 19:51:54.340263 INFO::Adjusting the last 2 batches sequentially
2024-11-07 19:51:54.341347 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 19:51:54.354581 INFO::Done
2024-11-07 19:51:54.355126 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:54.359758 INFO::ASW Batch was 0.467559324241701 prior to batch effect correction and is now 0.467559324241701 .
2024-11-07 19:51:54.360271 INFO::ASW Label was 0.346971940863632 prior to batch effect correction and is now 0.346971940863632 .
2024-11-07 19:51:54.360878 INFO::Total function execution time is 1.90961194038391 s and adjustment time is 1.86901497840881 s ( 97.87 )
2024-11-07 19:51:54.542279 INFO::Formatting Data.
2024-11-07 19:51:54.542955 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:54.544091 INFO::Removing potential empty rows and columns
2024-11-07 19:51:54.545267 INFO::Found 0 missing values.
2024-11-07 19:51:54.548606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:54.549063 INFO::Done
2024-11-07 19:51:54.549526 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 19:51:54.552281 INFO::Starting hierarchical adjustment
2024-11-07 19:51:54.552865 INFO::Found 3 batches.
2024-11-07 19:51:54.553303 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 19:51:54.553822 INFO::Using default BPPARAM
2024-11-07 19:51:54.554245 INFO::Processing subtree level 1
2024-11-07 19:51:54.665296 INFO::Adjusting the last 1 batches sequentially
2024-11-07 19:51:54.668091 INFO::Done
2024-11-07 19:51:54.668845 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 19:51:54.673071 INFO::ASW Batch was 0.20980361912389 prior to batch effect correction and is now -0.184911868515029 .
2024-11-07 19:51:54.673778 INFO::ASW Label was -0.213231505790194 prior to batch effect correction and is now -0.0427544317861352 .
2024-11-07 19:51:54.674963 INFO::Total function execution time is 0.132608890533447 s and adjustment time is 0.115306854248047 s ( 86.95 )
2024-11-07 19:51:54.847054 INFO::Formatting Data.
2024-11-07 19:51:54.848089 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:54.849177 INFO::Removing potential empty rows and columns
2024-11-07 19:51:54.850515 INFO::Found 2 missing values.
2024-11-07 19:51:54.853945 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:54.854584 INFO::Done
2024-11-07 19:51:54.894968 INFO::Found NA in Reference column
2024-11-07 19:51:54.908072 INFO::Require at least two references per batch.
2024-11-07 19:51:54.93658 INFO::Formatting Data.
2024-11-07 19:51:54.937403 INFO::Recognized SummarizedExperiment
2024-11-07 19:51:54.937992 INFO::Typecasting input to dataframe.
2024-11-07 19:51:54.951672 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:54.952971 INFO::Removing potential empty rows and columns
2024-11-07 19:51:54.957603 INFO::Found 0 missing values.
2024-11-07 19:51:54.966812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:54.967524 INFO::Done
2024-11-07 19:51:54.986965 INFO::Formatting Data.
2024-11-07 19:51:54.987784 INFO::Recognized SummarizedExperiment
2024-11-07 19:51:54.988394 INFO::Typecasting input to dataframe.
2024-11-07 19:51:55.00889 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:55.010259 INFO::Removing potential empty rows and columns
2024-11-07 19:51:55.015144 INFO::Found 0 missing values.
2024-11-07 19:51:55.029549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:55.030319 INFO::Done
2024-11-07 19:51:55.050081 INFO::Formatting Data.
2024-11-07 19:51:55.050893 INFO::Recognized SummarizedExperiment
2024-11-07 19:51:55.051504 INFO::Typecasting input to dataframe.
2024-11-07 19:51:55.07382 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:55.074961 INFO::Removing potential empty rows and columns
2024-11-07 19:51:55.076272 INFO::Found 0 missing values.
2024-11-07 19:51:55.077471 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.
2024-11-07 19:51:55.082932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:55.083651 INFO::Done
2024-11-07 19:51:55.099137 INFO::Formatting Data.
2024-11-07 19:51:55.099956 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:55.100972 INFO::Removing potential empty rows and columns
2024-11-07 19:51:55.102286 INFO::Found 0 missing values.
2024-11-07 19:51:55.106549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:55.10719 INFO::Done
2024-11-07 19:51:55.124267 INFO::Formatting Data.
2024-11-07 19:51:55.125212 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:55.126184 INFO::Removing potential empty rows and columns
2024-11-07 19:51:55.12733 INFO::Found 0 missing values.
2024-11-07 19:51:55.130711 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:55.131348 INFO::Done
2024-11-07 19:51:55.174529 INFO::Formatting Data.
2024-11-07 19:51:55.175496 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:55.177018 INFO::Removing potential empty rows and columns
2024-11-07 19:51:55.178308 INFO::Found 1 missing values.
2024-11-07 19:51:55.181208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:55.181764 INFO::Done
2024-11-07 19:51:55.208659 INFO::Formatting Data.
2024-11-07 19:51:55.209541 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:55.21055 INFO::Removing potential empty rows and columns
2024-11-07 19:51:55.211621 INFO::Found 2 missing values.
2024-11-07 19:51:55.212662 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.
2024-11-07 19:51:55.215241 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:55.215813 INFO::Done
2024-11-07 19:51:55.230513 INFO::Formatting Data.
2024-11-07 19:51:55.231606 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:55.232654 INFO::Removing potential empty rows and columns
2024-11-07 19:51:55.233688 INFO::Found 2 missing values.
2024-11-07 19:51:55.235504 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:55.236083 INFO::Done
2024-11-07 19:51:55.251776 INFO::Formatting Data.
2024-11-07 19:51:55.252696 INFO::Typecasting input to dataframe.
2024-11-07 19:51:55.253576 INFO::Replacing NaNs with NAs.
2024-11-07 19:51:55.254537 INFO::Removing potential empty rows and columns
2024-11-07 19:51:55.255665 INFO::Found 0 missing values.
2024-11-07 19:51:55.259274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 19:51:55.259887 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
15.236 3.196 18.679
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 19.657 | 1.014 | 14.061 | |
| compute_asw | 0.020 | 0.001 | 0.021 | |
| count_existing | 0.011 | 0.002 | 0.012 | |
| generate_data_covariables | 0.01 | 0.00 | 0.01 | |
| generate_dataset | 0.009 | 0.000 | 0.009 | |