Yannis Schumann
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 65b1ece |
| git_last_commit_date: 2024-02-28 02:41:28 -0400 (Wed, 28 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:36:12 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 155/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 0.99.16 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | 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: 0.99.16 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_0.99.16.tar.gz |
| StartedAt: 2024-03-27 20:30:13 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 20:31:42 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 89.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_0.99.16.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘0.99.16’
* 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 24.278 1.162 17.486
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-03-27 20:31:05.509526 INFO::Formatting Data.
2024-03-27 20:31:05.511019 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:05.521935 INFO::Removing potential empty rows and columns
2024-03-27 20:31:05.802539 INFO::Found 0 missing values.
2024-03-27 20:31:05.806276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:05.806929 INFO::Done
2024-03-27 20:31:05.807458 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:05.81977 INFO::Starting hierarchical adjustment
2024-03-27 20:31:05.820673 INFO::Found 3 batches.
2024-03-27 20:31:05.821188 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:05.822321 INFO::Using default BPPARAM
2024-03-27 20:31:05.822896 INFO::Processing subtree level 1
2024-03-27 20:31:05.920004 INFO::Adjusting the last 1 batches sequentially
2024-03-27 20:31:05.92194 INFO::Done
2024-03-27 20:31:05.922659 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:05.925528 INFO::ASW Batch was -0.0505502297907794 prior to batch effect correction and is now -0.0505502297907794 .
2024-03-27 20:31:05.926744 INFO::Total function execution time is 0.418042421340942 s and adjustment time is 0.101418972015381 s ( 24.26 )
2024-03-27 20:31:05.942359 INFO::Formatting Data.
2024-03-27 20:31:05.943227 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:05.944206 INFO::Removing potential empty rows and columns
2024-03-27 20:31:05.945323 INFO::Found 0 missing values.
2024-03-27 20:31:05.946327 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.
2024-03-27 20:31:05.958096 INFO::Formatting Data.
2024-03-27 20:31:05.958865 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:05.959811 INFO::Removing potential empty rows and columns
2024-03-27 20:31:05.960963 INFO::Found 0 missing values.
2024-03-27 20:31:05.961941 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.
2024-03-27 20:31:05.978429 INFO::Formatting Data.
2024-03-27 20:31:05.979184 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:05.980055 INFO::Removing potential empty rows and columns
2024-03-27 20:31:05.981052 INFO::Found 0 missing values.
2024-03-27 20:31:05.981951 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.
2024-03-27 20:31:05.986324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:05.98687 INFO::Done
2024-03-27 20:31:05.987379 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:05.989377 INFO::Starting hierarchical adjustment
2024-03-27 20:31:05.990056 INFO::Found 2 batches.
2024-03-27 20:31:05.990566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:05.991176 INFO::Using default BPPARAM
2024-03-27 20:31:05.991681 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:05.992625 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:06.015629 INFO::Done
2024-03-27 20:31:06.016379 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:06.018475 INFO::ASW Batch was -0.0126985767609541 prior to batch effect correction and is now -0.131205950392712 .
2024-03-27 20:31:06.019299 INFO::Total function execution time is 0.0409321784973145 s and adjustment time is 0.0256772041320801 s ( 62.73 )
2024-03-27 20:31:06.022218 INFO::Formatting Data.
2024-03-27 20:31:06.022848 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:06.031826 INFO::Formatting Data.
2024-03-27 20:31:06.032562 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:06.033439 INFO::Removing potential empty rows and columns
2024-03-27 20:31:06.034441 INFO::Found 0 missing values.
2024-03-27 20:31:06.037282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:06.037804 INFO::Done
2024-03-27 20:31:06.038305 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:06.040299 INFO::Starting hierarchical adjustment
2024-03-27 20:31:06.04097 INFO::Found 2 batches.
2024-03-27 20:31:06.041482 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:06.042087 INFO::Using default BPPARAM
2024-03-27 20:31:06.042581 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:06.043455 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:06.058164 INFO::Done
2024-03-27 20:31:06.058828 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:06.060814 INFO::ASW Batch was -0.0431953036404236 prior to batch effect correction and is now -0.125441562312341 .
2024-03-27 20:31:06.061582 INFO::Total function execution time is 0.0298316478729248 s and adjustment time is 0.0173225402832031 s ( 58.07 )
2024-03-27 20:31:06.062652 INFO::Formatting Data.
2024-03-27 20:31:06.06325 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:06.064112 INFO::Removing potential empty rows and columns
2024-03-27 20:31:06.065131 INFO::Found 0 missing values.
2024-03-27 20:31:06.067969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:06.068499 INFO::Done
2024-03-27 20:31:06.069037 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:06.07102 INFO::Starting hierarchical adjustment
2024-03-27 20:31:06.071689 INFO::Found 2 batches.
2024-03-27 20:31:06.072205 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:06.072786 INFO::Using default BPPARAM
2024-03-27 20:31:06.073287 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:06.074166 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:06.088912 INFO::Done
2024-03-27 20:31:06.089568 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:06.091558 INFO::ASW Batch was -0.0431953036404236 prior to batch effect correction and is now -0.125441562312341 .
2024-03-27 20:31:06.092335 INFO::Total function execution time is 0.029681921005249 s and adjustment time is 0.0173454284667969 s ( 58.44 )
2024-03-27 20:31:08.32343 INFO::Formatting Data.
2024-03-27 20:31:08.324208 INFO::Recognized SummarizedExperiment
2024-03-27 20:31:08.324736 INFO::Typecasting input to dataframe.
2024-03-27 20:31:08.38098 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:08.382106 INFO::Removing potential empty rows and columns
2024-03-27 20:31:08.385237 INFO::Found 0 missing values.
2024-03-27 20:31:08.390942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:08.391443 INFO::Done
2024-03-27 20:31:08.391886 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:08.39494 INFO::Starting hierarchical adjustment
2024-03-27 20:31:08.39555 INFO::Found 2 batches.
2024-03-27 20:31:08.396005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:08.396978 INFO::Using default BPPARAM
2024-03-27 20:31:08.397436 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:08.398289 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:08.445779 INFO::Done
2024-03-27 20:31:08.446412 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:08.449441 INFO::ASW Batch was -0.0133701774441644 prior to batch effect correction and is now -0.0904716448144669 .
2024-03-27 20:31:08.450163 INFO::Total function execution time is 0.127063989639282 s and adjustment time is 0.0503232479095459 s ( 39.6 )
2024-03-27 20:31:08.465435 INFO::Formatting Data.
2024-03-27 20:31:08.466077 INFO::Recognized SummarizedExperiment
2024-03-27 20:31:08.466575 INFO::Typecasting input to dataframe.
2024-03-27 20:31:08.474334 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:08.475367 INFO::Removing potential empty rows and columns
2024-03-27 20:31:08.4783 INFO::Found 0 missing values.
2024-03-27 20:31:08.483936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:08.48447 INFO::Done
2024-03-27 20:31:08.484931 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:08.487955 INFO::Starting hierarchical adjustment
2024-03-27 20:31:08.488666 INFO::Found 2 batches.
2024-03-27 20:31:08.489132 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:08.489662 INFO::Using default BPPARAM
2024-03-27 20:31:08.490122 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:08.491032 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:08.515483 INFO::Done
2024-03-27 20:31:08.516351 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:08.519708 INFO::ASW Batch was 0.00350990485116764 prior to batch effect correction and is now 0.00350990485116764 .
2024-03-27 20:31:08.520611 INFO::Total function execution time is 0.055142879486084 s and adjustment time is 0.0267558097839355 s ( 48.52 )
2024-03-27 20:31:08.539747 INFO::Formatting Data.
2024-03-27 20:31:08.540489 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:08.541325 INFO::Removing potential empty rows and columns
2024-03-27 20:31:08.542345 INFO::Found 0 missing values.
2024-03-27 20:31:08.545424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:08.545971 INFO::Done
2024-03-27 20:31:08.546551 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:08.548482 INFO::Starting hierarchical adjustment
2024-03-27 20:31:08.549087 INFO::Found 3 batches.
2024-03-27 20:31:08.549541 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:08.550127 INFO::Using default BPPARAM
2024-03-27 20:31:08.550578 INFO::Processing subtree level 1
2024-03-27 20:31:08.694672 INFO::Adjusting the last 1 batches sequentially
2024-03-27 20:31:08.696433 INFO::Done
2024-03-27 20:31:08.697035 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:08.699424 INFO::ASW Batch was -0.113194419186289 prior to batch effect correction and is now -0.164906316259168 .
2024-03-27 20:31:08.700371 INFO::Total function execution time is 0.160627603530884 s and adjustment time is 0.147440195083618 s ( 91.79 )
2024-03-27 20:31:08.71485 INFO::Skipping initial DF formatting
2024-03-27 20:31:08.715516 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:08.719593 INFO::Starting hierarchical adjustment
2024-03-27 20:31:08.720394 INFO::Found 5 batches.
2024-03-27 20:31:08.720907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:08.721541 INFO::Using default BPPARAM
2024-03-27 20:31:08.722059 INFO::Processing subtree level 1
2024-03-27 20:31:08.860151 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:08.861954 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:08.883209 INFO::Done
2024-03-27 20:31:08.884021 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:08.888409 INFO::ASW Batch was 0.515618748782925 prior to batch effect correction and is now 0.515618748782925 .
2024-03-27 20:31:08.889064 INFO::ASW Label was 0.378320851030593 prior to batch effect correction and is now 0.378320851030594 .
2024-03-27 20:31:08.889934 INFO::Total function execution time is 0.175148963928223 s and adjustment time is 0.162932872772217 s ( 93.03 )
2024-03-27 20:31:08.907947 INFO::Formatting Data.
2024-03-27 20:31:08.908811 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:08.909761 INFO::Removing potential empty rows and columns
2024-03-27 20:31:08.910769 INFO::Found 0 missing values.
2024-03-27 20:31:08.91512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:08.915668 INFO::Done
2024-03-27 20:31:08.916227 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:08.919332 INFO::Starting hierarchical adjustment
2024-03-27 20:31:08.920043 INFO::Found 5 batches.
2024-03-27 20:31:08.920585 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:08.921245 INFO::Using default BPPARAM
2024-03-27 20:31:08.921816 INFO::Processing subtree level 1
2024-03-27 20:31:09.046257 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:09.048043 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:09.065568 INFO::Done
2024-03-27 20:31:09.066373 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:09.06982 INFO::ASW Batch was 0.473024371790136 prior to batch effect correction and is now -0.0825161345986663 .
2024-03-27 20:31:09.070436 INFO::ASW Label was 0.296732902043029 prior to batch effect correction and is now 0.78006984748644 .
2024-03-27 20:31:09.071255 INFO::Total function execution time is 0.163427591323853 s and adjustment time is 0.145646810531616 s ( 89.12 )
2024-03-27 20:31:09.072117 INFO::Formatting Data.
2024-03-27 20:31:09.072729 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:09.07364 INFO::Removing potential empty rows and columns
2024-03-27 20:31:09.07462 INFO::Found 0 missing values.
2024-03-27 20:31:09.078622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:09.079153 INFO::Done
2024-03-27 20:31:09.079668 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:09.082613 INFO::Starting hierarchical adjustment
2024-03-27 20:31:09.083308 INFO::Found 5 batches.
2024-03-27 20:31:09.083856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:09.084523 INFO::Using default BPPARAM
2024-03-27 20:31:09.085052 INFO::Processing subtree level 1
2024-03-27 20:31:09.196718 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:09.198259 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:09.213594 INFO::Done
2024-03-27 20:31:09.214315 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:09.217469 INFO::ASW Batch was 0.473024371790136 prior to batch effect correction and is now -0.0825161345986663 .
2024-03-27 20:31:09.218056 INFO::ASW Label was 0.296732902043029 prior to batch effect correction and is now 0.78006984748644 .
2024-03-27 20:31:09.218851 INFO::Total function execution time is 0.146751165390015 s and adjustment time is 0.130392074584961 s ( 88.85 )
2024-03-27 20:31:09.231669 INFO::Formatting Data.
2024-03-27 20:31:09.23244 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:09.233345 INFO::Removing potential empty rows and columns
2024-03-27 20:31:09.234314 INFO::Found 0 missing values.
2024-03-27 20:31:09.238263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:09.238792 INFO::Done
2024-03-27 20:31:09.23931 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:09.242287 INFO::Starting hierarchical adjustment
2024-03-27 20:31:09.242991 INFO::Found 5 batches.
2024-03-27 20:31:09.243506 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:09.244144 INFO::Using default BPPARAM
2024-03-27 20:31:09.244665 INFO::Processing subtree level 1
2024-03-27 20:31:09.381647 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:09.383488 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:09.399968 INFO::Done
2024-03-27 20:31:09.40072 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:09.403996 INFO::ASW Batch was 0.570816396531087 prior to batch effect correction and is now -0.0270122690877942 .
2024-03-27 20:31:09.404631 INFO::ASW Label was 0.236433263626939 prior to batch effect correction and is now 0.736709749105269 .
2024-03-27 20:31:09.405488 INFO::Total function execution time is 0.173872709274292 s and adjustment time is 0.157095909118652 s ( 90.35 )
2024-03-27 20:31:09.406356 INFO::Formatting Data.
2024-03-27 20:31:09.406983 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:09.407899 INFO::Removing potential empty rows and columns
2024-03-27 20:31:09.408946 INFO::Found 0 missing values.
2024-03-27 20:31:09.413136 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:09.413698 INFO::Done
2024-03-27 20:31:09.414234 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:09.417268 INFO::Starting hierarchical adjustment
2024-03-27 20:31:09.41801 INFO::Found 5 batches.
2024-03-27 20:31:09.418546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:09.419197 INFO::Using default BPPARAM
2024-03-27 20:31:09.419726 INFO::Processing subtree level 1
2024-03-27 20:31:09.543689 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:09.545695 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:09.564889 INFO::Done
2024-03-27 20:31:09.565733 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:09.569487 INFO::ASW Batch was 0.570816396531087 prior to batch effect correction and is now -0.0270122690877942 .
2024-03-27 20:31:09.570185 INFO::ASW Label was 0.236433263626939 prior to batch effect correction and is now 0.736709749105269 .
2024-03-27 20:31:09.571523 INFO::Total function execution time is 0.165050029754639 s and adjustment time is 0.146985530853271 s ( 89.06 )
2024-03-27 20:31:09.585186 INFO::Formatting Data.
2024-03-27 20:31:09.586058 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:09.587052 INFO::Removing potential empty rows and columns
2024-03-27 20:31:09.588131 INFO::Found 0 missing values.
2024-03-27 20:31:09.591008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:09.591565 INFO::Done
2024-03-27 20:31:09.592132 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:09.595235 INFO::Starting hierarchical adjustment
2024-03-27 20:31:09.595963 INFO::Found 2 batches.
2024-03-27 20:31:09.596505 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:09.597171 INFO::Using default BPPARAM
2024-03-27 20:31:09.597716 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:09.598657 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:09.614099 INFO::Done
2024-03-27 20:31:09.614805 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:09.617748 INFO::ASW Batch was 0.687487860980361 prior to batch effect correction and is now -0.0355178953548542 .
2024-03-27 20:31:09.618325 INFO::ASW Label was 0.380233850484622 prior to batch effect correction and is now 0.928029843652423 .
2024-03-27 20:31:09.6191 INFO::Total function execution time is 0.0340421199798584 s and adjustment time is 0.0182812213897705 s ( 53.7 )
2024-03-27 20:31:09.619877 INFO::Formatting Data.
2024-03-27 20:31:09.620489 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:09.621377 INFO::Removing potential empty rows and columns
2024-03-27 20:31:09.622339 INFO::Found 0 missing values.
2024-03-27 20:31:09.625014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:09.625558 INFO::Done
2024-03-27 20:31:09.626069 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:09.628964 INFO::Starting hierarchical adjustment
2024-03-27 20:31:09.629657 INFO::Found 2 batches.
2024-03-27 20:31:09.630175 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:09.630858 INFO::Using default BPPARAM
2024-03-27 20:31:09.631387 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:09.632302 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:09.670481 INFO::Done
2024-03-27 20:31:09.671239 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:09.674344 INFO::ASW Batch was 0.687487860980361 prior to batch effect correction and is now -0.0355178953548542 .
2024-03-27 20:31:09.674917 INFO::ASW Label was 0.380233850484622 prior to batch effect correction and is now 0.928029843652423 .
2024-03-27 20:31:09.675734 INFO::Total function execution time is 0.0558676719665527 s and adjustment time is 0.0409388542175293 s ( 73.28 )
2024-03-27 20:31:09.686594 INFO::Formatting Data.
2024-03-27 20:31:09.687328 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:09.688258 INFO::Removing potential empty rows and columns
2024-03-27 20:31:09.689149 INFO::Found 0 missing values.
2024-03-27 20:31:09.691184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:09.69171 INFO::Done
2024-03-27 20:31:09.692215 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:09.694085 INFO::Starting hierarchical adjustment
2024-03-27 20:31:09.694748 INFO::Found 2 batches.
2024-03-27 20:31:09.695248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:09.695817 INFO::Using default BPPARAM
2024-03-27 20:31:09.696341 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:09.697215 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:09.73417 INFO::Done
2024-03-27 20:31:09.734983 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:09.737146 INFO::ASW Batch was 0.00368027183865821 prior to batch effect correction and is now -0.0651475871996678 .
2024-03-27 20:31:09.738009 INFO::Total function execution time is 0.051478385925293 s and adjustment time is 0.0395164489746094 s ( 76.76 )
2024-03-27 20:31:09.750462 INFO::Formatting Data.
2024-03-27 20:31:09.751242 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:09.752163 INFO::Removing potential empty rows and columns
2024-03-27 20:31:09.753218 INFO::Found 0 missing values.
2024-03-27 20:31:09.754493 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.
2024-03-27 20:31:09.759383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:09.759998 INFO::Done
2024-03-27 20:31:09.760507 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:09.763624 INFO::Starting hierarchical adjustment
2024-03-27 20:31:09.764367 INFO::Found 2 batches.
2024-03-27 20:31:09.764872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:09.765465 INFO::Using default BPPARAM
2024-03-27 20:31:09.766007 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:09.767007 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:09.785512 INFO::Done
2024-03-27 20:31:09.786179 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:09.789206 INFO::ASW Batch was 0.522210922420301 prior to batch effect correction and is now 0.0959666463773984 .
2024-03-27 20:31:09.789763 INFO::ASW Label was 0.566062318789594 prior to batch effect correction and is now 0.881413606877634 .
2024-03-27 20:31:09.790527 INFO::Total function execution time is 0.0401613712310791 s and adjustment time is 0.0212924480438232 s ( 53.02 )
2024-03-27 20:31:09.791292 INFO::Formatting Data.
2024-03-27 20:31:09.791888 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:09.792819 INFO::Removing potential empty rows and columns
2024-03-27 20:31:09.793806 INFO::Found 0 missing values.
2024-03-27 20:31:09.794698 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.
2024-03-27 20:31:09.799407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:09.799935 INFO::Done
2024-03-27 20:31:09.800458 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:09.803398 INFO::Starting hierarchical adjustment
2024-03-27 20:31:09.804095 INFO::Found 2 batches.
2024-03-27 20:31:09.804604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:09.805192 INFO::Using default BPPARAM
2024-03-27 20:31:09.805701 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:09.806624 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:09.824017 INFO::Done
2024-03-27 20:31:09.824691 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:09.827493 INFO::ASW Batch was 0.522210922420301 prior to batch effect correction and is now 0.0959666463773984 .
2024-03-27 20:31:09.828068 INFO::ASW Label was 0.566062318789594 prior to batch effect correction and is now 0.881413606877634 .
2024-03-27 20:31:09.828819 INFO::Total function execution time is 0.0375447273254395 s and adjustment time is 0.0200350284576416 s ( 53.36 )
2024-03-27 20:31:10.036692 INFO::Formatting Data.
2024-03-27 20:31:10.037485 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:10.038363 INFO::Removing potential empty rows and columns
2024-03-27 20:31:10.039344 INFO::Found 0 missing values.
2024-03-27 20:31:10.042339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:10.042848 INFO::Done
2024-03-27 20:31:10.04335 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:10.045306 INFO::Starting hierarchical adjustment
2024-03-27 20:31:10.045996 INFO::Found 3 batches.
2024-03-27 20:31:10.046506 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:10.047126 INFO::Using default BPPARAM
2024-03-27 20:31:10.047638 INFO::Processing subtree level 1
2024-03-27 20:31:10.153767 INFO::Adjusting the last 1 batches sequentially
2024-03-27 20:31:10.155616 INFO::Done
2024-03-27 20:31:10.156286 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:10.158859 INFO::ASW Batch was -0.0528001275276268 prior to batch effect correction and is now -0.0528001275276268 .
2024-03-27 20:31:10.159813 INFO::Total function execution time is 0.123140573501587 s and adjustment time is 0.109745979309082 s ( 89.12 )
2024-03-27 20:31:10.160974 INFO::Formatting Data.
2024-03-27 20:31:10.161701 INFO::Typecasting input to dataframe.
2024-03-27 20:31:10.162529 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:10.1635 INFO::Removing potential empty rows and columns
2024-03-27 20:31:10.164587 INFO::Found 0 missing values.
2024-03-27 20:31:10.167577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:10.168153 INFO::Done
2024-03-27 20:31:10.168678 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:10.170621 INFO::Starting hierarchical adjustment
2024-03-27 20:31:10.171325 INFO::Found 3 batches.
2024-03-27 20:31:10.171853 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:10.172481 INFO::Using default BPPARAM
2024-03-27 20:31:10.173015 INFO::Processing subtree level 1
2024-03-27 20:31:10.266847 INFO::Adjusting the last 1 batches sequentially
2024-03-27 20:31:10.270481 INFO::Done
2024-03-27 20:31:10.271463 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:10.274197 INFO::ASW Batch was -0.0528001275276268 prior to batch effect correction and is now -0.0528001275276268 .
2024-03-27 20:31:10.275261 INFO::Total function execution time is 0.114282846450806 s and adjustment time is 0.0990676879882812 s ( 86.69 )
2024-03-27 20:31:10.288939 INFO::Formatting Data.
2024-03-27 20:31:10.289767 INFO::Typecasting input to dataframe.
2024-03-27 20:31:10.290617 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:10.291574 INFO::Removing potential empty rows and columns
2024-03-27 20:31:10.292726 INFO::Found 0 missing values.
2024-03-27 20:31:10.295679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:10.296252 INFO::Done
2024-03-27 20:31:10.29678 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:10.298764 INFO::Starting hierarchical adjustment
2024-03-27 20:31:10.29947 INFO::Found 3 batches.
2024-03-27 20:31:10.299999 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:10.300702 INFO::Using default BPPARAM
2024-03-27 20:31:10.301225 INFO::Processing subtree level 1
2024-03-27 20:31:10.409561 INFO::Adjusting the last 1 batches sequentially
2024-03-27 20:31:10.41175 INFO::Done
2024-03-27 20:31:10.412534 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:10.415483 INFO::ASW Batch was -0.0892013806565161 prior to batch effect correction and is now -0.0892013806565161 .
2024-03-27 20:31:10.41661 INFO::Total function execution time is 0.127679109573364 s and adjustment time is 0.112409114837646 s ( 88.04 )
2024-03-27 20:31:10.609619 INFO::Formatting Data.
2024-03-27 20:31:10.610437 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:10.611638 INFO::Removing potential empty rows and columns
2024-03-27 20:31:10.614606 INFO::Found 1000 missing values.
2024-03-27 20:31:10.634162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:10.634905 INFO::Done
2024-03-27 20:31:10.635483 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:10.665862 INFO::Starting hierarchical adjustment
2024-03-27 20:31:10.666806 INFO::Found 10 batches.
2024-03-27 20:31:10.667416 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:10.668167 INFO::Using default BPPARAM
2024-03-27 20:31:10.668743 INFO::Processing subtree level 1
2024-03-27 20:31:10.831975 INFO::Processing subtree level 2
2024-03-27 20:31:11.023418 INFO::Adjusting the last 1 batches sequentially
2024-03-27 20:31:11.025821 INFO::Done
2024-03-27 20:31:11.026661 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:11.034223 INFO::ASW Batch was 0.500134560474489 prior to batch effect correction and is now 0.500134560474489 .
2024-03-27 20:31:11.035324 INFO::ASW Label was 0.314086671010086 prior to batch effect correction and is now 0.314086671010086 .
2024-03-27 20:31:11.036488 INFO::Total function execution time is 0.426876544952393 s and adjustment time is 0.359165906906128 s ( 84.14 )
2024-03-27 20:31:11.037564 INFO::Formatting Data.
2024-03-27 20:31:11.038335 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:11.039956 INFO::Removing potential empty rows and columns
2024-03-27 20:31:11.043554 INFO::Found 1000 missing values.
2024-03-27 20:31:11.070817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:11.071963 INFO::Done
2024-03-27 20:31:11.072714 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:11.079772 INFO::Starting hierarchical adjustment
2024-03-27 20:31:11.080753 INFO::Found 10 batches.
2024-03-27 20:31:12.216939 INFO::Set up parallel execution backend with 2 workers
2024-03-27 20:31:12.218477 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-03-27 20:31:13.287461 INFO::Adjusting the last 2 batches sequentially
2024-03-27 20:31:13.289278 INFO::Adjusting sequential tree level 1 with 2 batches
2024-03-27 20:31:13.306057 INFO::Done
2024-03-27 20:31:13.306774 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:13.311852 INFO::ASW Batch was 0.500134560474489 prior to batch effect correction and is now 0.500134560474489 .
2024-03-27 20:31:13.312437 INFO::ASW Label was 0.314086671010086 prior to batch effect correction and is now 0.314086671010086 .
2024-03-27 20:31:13.313228 INFO::Total function execution time is 2.27571940422058 s and adjustment time is 2.22553443908691 s ( 97.79 )
2024-03-27 20:31:13.44503 INFO::Formatting Data.
2024-03-27 20:31:13.44578 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.446651 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.447624 INFO::Found 0 missing values.
2024-03-27 20:31:13.451039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.451563 INFO::Done
2024-03-27 20:31:13.452064 INFO::Acquiring quality metrics before batch effect correction.
2024-03-27 20:31:13.454645 INFO::Starting hierarchical adjustment
2024-03-27 20:31:13.455287 INFO::Found 3 batches.
2024-03-27 20:31:13.455777 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-03-27 20:31:13.45637 INFO::Using default BPPARAM
2024-03-27 20:31:13.456891 INFO::Processing subtree level 1
2024-03-27 20:31:13.564991 INFO::Adjusting the last 1 batches sequentially
2024-03-27 20:31:13.567322 INFO::Done
2024-03-27 20:31:13.568094 INFO::Acquiring quality metrics after batch effect correction.
2024-03-27 20:31:13.571785 INFO::ASW Batch was 0.148164428319363 prior to batch effect correction and is now -0.130597485510462 .
2024-03-27 20:31:13.572496 INFO::ASW Label was -0.209424143448787 prior to batch effect correction and is now 0.00865694579919913 .
2024-03-27 20:31:13.573551 INFO::Total function execution time is 0.12851881980896 s and adjustment time is 0.112112760543823 s ( 87.23 )
2024-03-27 20:31:13.686904 INFO::Formatting Data.
2024-03-27 20:31:13.68768 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.688557 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.689544 INFO::Found 2 missing values.
2024-03-27 20:31:13.692243 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.692759 INFO::Done
2024-03-27 20:31:13.717395 INFO::Found NA in Reference column
2024-03-27 20:31:13.726112 INFO::Require at least two references per batch.
2024-03-27 20:31:13.745003 INFO::Formatting Data.
2024-03-27 20:31:13.745723 INFO::Recognized SummarizedExperiment
2024-03-27 20:31:13.746241 INFO::Typecasting input to dataframe.
2024-03-27 20:31:13.755204 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.75629 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.759546 INFO::Found 0 missing values.
2024-03-27 20:31:13.766017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.766608 INFO::Done
2024-03-27 20:31:13.781063 INFO::Formatting Data.
2024-03-27 20:31:13.781763 INFO::Recognized SummarizedExperiment
2024-03-27 20:31:13.782286 INFO::Typecasting input to dataframe.
2024-03-27 20:31:13.798938 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.800153 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.803521 INFO::Found 0 missing values.
2024-03-27 20:31:13.814029 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.81465 INFO::Done
2024-03-27 20:31:13.829416 INFO::Formatting Data.
2024-03-27 20:31:13.830124 INFO::Recognized SummarizedExperiment
2024-03-27 20:31:13.830639 INFO::Typecasting input to dataframe.
2024-03-27 20:31:13.846868 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.84789 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.84895 INFO::Found 0 missing values.
2024-03-27 20:31:13.849941 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.
2024-03-27 20:31:13.854262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.854779 INFO::Done
2024-03-27 20:31:13.86456 INFO::Formatting Data.
2024-03-27 20:31:13.86533 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.866233 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.867231 INFO::Found 0 missing values.
2024-03-27 20:31:13.870074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.870602 INFO::Done
2024-03-27 20:31:13.881123 INFO::Formatting Data.
2024-03-27 20:31:13.881886 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.882832 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.883781 INFO::Found 0 missing values.
2024-03-27 20:31:13.886562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.887072 INFO::Done
2024-03-27 20:31:13.92193 INFO::Formatting Data.
2024-03-27 20:31:13.922954 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.924113 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.925362 INFO::Found 1 missing values.
2024-03-27 20:31:13.928014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.928724 INFO::Done
2024-03-27 20:31:13.947814 INFO::Formatting Data.
2024-03-27 20:31:13.948663 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.949663 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.950706 INFO::Found 2 missing values.
2024-03-27 20:31:13.951719 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.
2024-03-27 20:31:13.954271 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.954874 INFO::Done
2024-03-27 20:31:13.96581 INFO::Formatting Data.
2024-03-27 20:31:13.966616 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.967514 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.968479 INFO::Found 2 missing values.
2024-03-27 20:31:13.970263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.970822 INFO::Done
2024-03-27 20:31:13.982164 INFO::Formatting Data.
2024-03-27 20:31:13.982991 INFO::Typecasting input to dataframe.
2024-03-27 20:31:13.983861 INFO::Replacing NaNs with NAs.
2024-03-27 20:31:13.984779 INFO::Removing potential empty rows and columns
2024-03-27 20:31:13.985872 INFO::Found 0 missing values.
2024-03-27 20:31:13.989384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-03-27 20:31:13.98995 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.985 3.742 20.435
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.278 | 1.162 | 17.486 | |
| compute_asw | 0.023 | 0.003 | 0.026 | |
| count_existing | 0.015 | 0.000 | 0.016 | |
| generate_data_covariables | 0.013 | 0.000 | 0.014 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |