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 12:03 -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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz |
| StartedAt: 2024-11-07 20:27:18 -0500 (Thu, 07 Nov 2024) |
| EndedAt: 2024-11-07 20:32:28 -0500 (Thu, 07 Nov 2024) |
| EllapsedTime: 309.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...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 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 21.239 1.34 15.608
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-11-07 20:31:54.593103 INFO::Formatting Data.
2024-11-07 20:31:54.594345 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:54.605422 INFO::Removing potential empty rows and columns
2024-11-07 20:31:54.851868 INFO::Found 0 missing values.
2024-11-07 20:31:54.85515 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:54.855766 INFO::Done
2024-11-07 20:31:54.856267 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:54.867348 INFO::Starting hierarchical adjustment
2024-11-07 20:31:54.868175 INFO::Found 3 batches.
2024-11-07 20:31:54.868722 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:54.869865 INFO::Using default BPPARAM
2024-11-07 20:31:54.870417 INFO::Processing subtree level 1
2024-11-07 20:31:54.966938 INFO::Adjusting the last 1 batches sequentially
2024-11-07 20:31:54.968629 INFO::Done
2024-11-07 20:31:54.969289 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:54.97181 INFO::ASW Batch was -0.0296001491323741 prior to batch effect correction and is now -0.0296001491323741 .
2024-11-07 20:31:54.972869 INFO::Total function execution time is 0.380421876907349 s and adjustment time is 0.100631713867188 s ( 26.45 )
2024-11-07 20:31:54.986123 INFO::Formatting Data.
2024-11-07 20:31:54.986842 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:54.987707 INFO::Removing potential empty rows and columns
2024-11-07 20:31:54.98877 INFO::Found 0 missing values.
2024-11-07 20:31:54.9897 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 20:31:55.000222 INFO::Formatting Data.
2024-11-07 20:31:55.000836 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:55.001641 INFO::Removing potential empty rows and columns
2024-11-07 20:31:55.002666 INFO::Found 0 missing values.
2024-11-07 20:31:55.003525 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 20:31:55.018723 INFO::Formatting Data.
2024-11-07 20:31:55.019329 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:55.020123 INFO::Removing potential empty rows and columns
2024-11-07 20:31:55.021093 INFO::Found 0 missing values.
2024-11-07 20:31:55.021954 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 20:31:55.02637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:55.026891 INFO::Done
2024-11-07 20:31:55.027382 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:55.02939 INFO::Starting hierarchical adjustment
2024-11-07 20:31:55.030106 INFO::Found 2 batches.
2024-11-07 20:31:55.030617 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:55.031237 INFO::Using default BPPARAM
2024-11-07 20:31:55.031761 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:55.032751 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:55.054273 INFO::Done
2024-11-07 20:31:55.05493 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:55.05686 INFO::ASW Batch was -0.000327507754803488 prior to batch effect correction and is now -0.0741297719860028 .
2024-11-07 20:31:55.057609 INFO::Total function execution time is 0.0389044284820557 s and adjustment time is 0.0242946147918701 s ( 62.45 )
2024-11-07 20:31:55.06027 INFO::Formatting Data.
2024-11-07 20:31:55.060863 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:55.06931 INFO::Formatting Data.
2024-11-07 20:31:55.069982 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:55.070876 INFO::Removing potential empty rows and columns
2024-11-07 20:31:55.071957 INFO::Found 0 missing values.
2024-11-07 20:31:55.074752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:55.075271 INFO::Done
2024-11-07 20:31:55.075824 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:55.077897 INFO::Starting hierarchical adjustment
2024-11-07 20:31:55.078591 INFO::Found 2 batches.
2024-11-07 20:31:55.079127 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:55.07971 INFO::Using default BPPARAM
2024-11-07 20:31:55.080218 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:55.081128 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:55.095622 INFO::Done
2024-11-07 20:31:55.096188 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:55.098022 INFO::ASW Batch was -0.0342979561427871 prior to batch effect correction and is now -0.108885228106088 .
2024-11-07 20:31:55.098752 INFO::Total function execution time is 0.0294475555419922 s and adjustment time is 0.0171780586242676 s ( 58.33 )
2024-11-07 20:31:55.099741 INFO::Formatting Data.
2024-11-07 20:31:55.100301 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:55.101105 INFO::Removing potential empty rows and columns
2024-11-07 20:31:55.102071 INFO::Found 0 missing values.
2024-11-07 20:31:55.10484 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:55.105337 INFO::Done
2024-11-07 20:31:55.105823 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:55.107715 INFO::Starting hierarchical adjustment
2024-11-07 20:31:55.108365 INFO::Found 2 batches.
2024-11-07 20:31:55.108859 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:55.109421 INFO::Using default BPPARAM
2024-11-07 20:31:55.109911 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:55.110752 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:55.125214 INFO::Done
2024-11-07 20:31:55.125803 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:55.127705 INFO::ASW Batch was -0.0342979561427871 prior to batch effect correction and is now -0.108885228106088 .
2024-11-07 20:31:55.128455 INFO::Total function execution time is 0.028724193572998 s and adjustment time is 0.0169744491577148 s ( 59.09 )
2024-11-07 20:31:57.159148 INFO::Formatting Data.
2024-11-07 20:31:57.159839 INFO::Recognized SummarizedExperiment
2024-11-07 20:31:57.160281 INFO::Typecasting input to dataframe.
2024-11-07 20:31:57.198631 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:57.199773 INFO::Removing potential empty rows and columns
2024-11-07 20:31:57.20295 INFO::Found 0 missing values.
2024-11-07 20:31:57.208751 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:57.209216 INFO::Done
2024-11-07 20:31:57.209636 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:57.212615 INFO::Starting hierarchical adjustment
2024-11-07 20:31:57.21321 INFO::Found 2 batches.
2024-11-07 20:31:57.213643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:57.214609 INFO::Using default BPPARAM
2024-11-07 20:31:57.215093 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:57.215961 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:57.269047 INFO::Done
2024-11-07 20:31:57.269626 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:57.272724 INFO::ASW Batch was -0.013197038161228 prior to batch effect correction and is now -0.0900616152470588 .
2024-11-07 20:31:57.273432 INFO::Total function execution time is 0.11461329460144 s and adjustment time is 0.0559446811676025 s ( 48.81 )
2024-11-07 20:31:57.289685 INFO::Formatting Data.
2024-11-07 20:31:57.290251 INFO::Recognized SummarizedExperiment
2024-11-07 20:31:57.290695 INFO::Typecasting input to dataframe.
2024-11-07 20:31:57.298543 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:57.299484 INFO::Removing potential empty rows and columns
2024-11-07 20:31:57.302477 INFO::Found 0 missing values.
2024-11-07 20:31:57.308154 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:57.308602 INFO::Done
2024-11-07 20:31:57.309033 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:57.311892 INFO::Starting hierarchical adjustment
2024-11-07 20:31:57.312477 INFO::Found 2 batches.
2024-11-07 20:31:57.312945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:57.313435 INFO::Using default BPPARAM
2024-11-07 20:31:57.313874 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:57.314672 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:57.335085 INFO::Done
2024-11-07 20:31:57.335625 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:57.338504 INFO::ASW Batch was -0.0124874833755108 prior to batch effect correction and is now -0.0124874833755108 .
2024-11-07 20:31:57.339208 INFO::Total function execution time is 0.0495011806488037 s and adjustment time is 0.0227160453796387 s ( 45.89 )
2024-11-07 20:31:57.35403 INFO::Formatting Data.
2024-11-07 20:31:57.354625 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:57.355374 INFO::Removing potential empty rows and columns
2024-11-07 20:31:57.356214 INFO::Found 0 missing values.
2024-11-07 20:31:57.358768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:57.359245 INFO::Done
2024-11-07 20:31:57.359704 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:57.361488 INFO::Starting hierarchical adjustment
2024-11-07 20:31:57.362205 INFO::Found 3 batches.
2024-11-07 20:31:57.362719 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:57.363246 INFO::Using default BPPARAM
2024-11-07 20:31:57.363708 INFO::Processing subtree level 1
2024-11-07 20:31:57.509778 INFO::Adjusting the last 1 batches sequentially
2024-11-07 20:31:57.511477 INFO::Done
2024-11-07 20:31:57.512089 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:57.514456 INFO::ASW Batch was 0.0317815402866401 prior to batch effect correction and is now -0.16012971633829 .
2024-11-07 20:31:57.515333 INFO::Total function execution time is 0.161262512207031 s and adjustment time is 0.149392127990723 s ( 92.64 )
2024-11-07 20:31:57.52983 INFO::Skipping initial DF formatting
2024-11-07 20:31:57.530446 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:57.534359 INFO::Starting hierarchical adjustment
2024-11-07 20:31:57.535106 INFO::Found 5 batches.
2024-11-07 20:31:57.535622 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:57.536242 INFO::Using default BPPARAM
2024-11-07 20:31:57.536759 INFO::Processing subtree level 1
2024-11-07 20:31:57.697216 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:57.698877 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:57.721506 INFO::Done
2024-11-07 20:31:57.722223 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:57.726176 INFO::ASW Batch was 0.525432741671738 prior to batch effect correction and is now 0.525432741671738 .
2024-11-07 20:31:57.726743 INFO::ASW Label was 0.3954243479239 prior to batch effect correction and is now 0.3954243479239 .
2024-11-07 20:31:57.727552 INFO::Total function execution time is 0.197788000106812 s and adjustment time is 0.186541557312012 s ( 94.31 )
2024-11-07 20:31:57.743919 INFO::Formatting Data.
2024-11-07 20:31:57.744571 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:57.745415 INFO::Removing potential empty rows and columns
2024-11-07 20:31:57.746345 INFO::Found 0 missing values.
2024-11-07 20:31:57.750226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:57.750735 INFO::Done
2024-11-07 20:31:57.751228 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:57.753981 INFO::Starting hierarchical adjustment
2024-11-07 20:31:57.75466 INFO::Found 5 batches.
2024-11-07 20:31:57.755184 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:57.755778 INFO::Using default BPPARAM
2024-11-07 20:31:57.756294 INFO::Processing subtree level 1
2024-11-07 20:31:57.89201 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:57.893817 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:57.91026 INFO::Done
2024-11-07 20:31:57.910969 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:57.914014 INFO::ASW Batch was 0.412296203877507 prior to batch effect correction and is now -0.0464137048677443 .
2024-11-07 20:31:57.914613 INFO::ASW Label was 0.369918089865213 prior to batch effect correction and is now 0.809976470186695 .
2024-11-07 20:31:57.915401 INFO::Total function execution time is 0.171522855758667 s and adjustment time is 0.155715465545654 s ( 90.78 )
2024-11-07 20:31:57.91619 INFO::Formatting Data.
2024-11-07 20:31:57.916792 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:57.917615 INFO::Removing potential empty rows and columns
2024-11-07 20:31:57.91854 INFO::Found 0 missing values.
2024-11-07 20:31:57.922418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:57.92295 INFO::Done
2024-11-07 20:31:57.923526 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:57.92632 INFO::Starting hierarchical adjustment
2024-11-07 20:31:57.926999 INFO::Found 5 batches.
2024-11-07 20:31:57.927499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:57.928091 INFO::Using default BPPARAM
2024-11-07 20:31:57.928602 INFO::Processing subtree level 1
2024-11-07 20:31:58.058921 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:58.060561 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:58.07625 INFO::Done
2024-11-07 20:31:58.076998 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:58.080285 INFO::ASW Batch was 0.412296203877507 prior to batch effect correction and is now -0.0464137048677443 .
2024-11-07 20:31:58.080917 INFO::ASW Label was 0.369918089865213 prior to batch effect correction and is now 0.809976470186695 .
2024-11-07 20:31:58.082314 INFO::Total function execution time is 0.165525674819946 s and adjustment time is 0.149354457855225 s ( 90.23 )
2024-11-07 20:31:58.097164 INFO::Formatting Data.
2024-11-07 20:31:58.098009 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:58.098981 INFO::Removing potential empty rows and columns
2024-11-07 20:31:58.100047 INFO::Found 0 missing values.
2024-11-07 20:31:58.104314 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:58.104871 INFO::Done
2024-11-07 20:31:58.105377 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:58.108499 INFO::Starting hierarchical adjustment
2024-11-07 20:31:58.109215 INFO::Found 5 batches.
2024-11-07 20:31:58.109735 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:58.110352 INFO::Using default BPPARAM
2024-11-07 20:31:58.110906 INFO::Processing subtree level 1
2024-11-07 20:31:58.306463 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:58.308151 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:58.324836 INFO::Done
2024-11-07 20:31:58.325642 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:58.32912 INFO::ASW Batch was 0.650099532772641 prior to batch effect correction and is now -0.0893595140817526 .
2024-11-07 20:31:58.329794 INFO::ASW Label was 0.145370212798085 prior to batch effect correction and is now 0.795530275979459 .
2024-11-07 20:31:58.330732 INFO::Total function execution time is 0.233671426773071 s and adjustment time is 0.215719938278198 s ( 92.32 )
2024-11-07 20:31:58.331637 INFO::Formatting Data.
2024-11-07 20:31:58.332298 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:58.33323 INFO::Removing potential empty rows and columns
2024-11-07 20:31:58.334611 INFO::Found 0 missing values.
2024-11-07 20:31:58.361926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:58.362669 INFO::Done
2024-11-07 20:31:58.363217 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:58.366386 INFO::Starting hierarchical adjustment
2024-11-07 20:31:58.367131 INFO::Found 5 batches.
2024-11-07 20:31:58.367646 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:58.368247 INFO::Using default BPPARAM
2024-11-07 20:31:58.368765 INFO::Processing subtree level 1
2024-11-07 20:31:58.50184 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:58.503501 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:58.520291 INFO::Done
2024-11-07 20:31:58.520958 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:58.524407 INFO::ASW Batch was 0.650099532772641 prior to batch effect correction and is now -0.0893595140817526 .
2024-11-07 20:31:58.525004 INFO::ASW Label was 0.145370212798085 prior to batch effect correction and is now 0.795530275979459 .
2024-11-07 20:31:58.525856 INFO::Total function execution time is 0.194209098815918 s and adjustment time is 0.153322458267212 s ( 78.95 )
2024-11-07 20:31:58.53966 INFO::Formatting Data.
2024-11-07 20:31:58.540394 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:58.541325 INFO::Removing potential empty rows and columns
2024-11-07 20:31:58.542386 INFO::Found 0 missing values.
2024-11-07 20:31:58.545148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:58.545689 INFO::Done
2024-11-07 20:31:58.546192 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:58.549319 INFO::Starting hierarchical adjustment
2024-11-07 20:31:58.550025 INFO::Found 2 batches.
2024-11-07 20:31:58.550538 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:58.551158 INFO::Using default BPPARAM
2024-11-07 20:31:58.551686 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:58.552554 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:58.567221 INFO::Done
2024-11-07 20:31:58.567805 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:58.570688 INFO::ASW Batch was 0.499670140526149 prior to batch effect correction and is now -0.00613586648565829 .
2024-11-07 20:31:58.571226 INFO::ASW Label was 0.564206481435545 prior to batch effect correction and is now 0.8987386318606 .
2024-11-07 20:31:58.57196 INFO::Total function execution time is 0.0323669910430908 s and adjustment time is 0.0173416137695312 s ( 53.58 )
2024-11-07 20:31:58.572693 INFO::Formatting Data.
2024-11-07 20:31:58.573267 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:58.57409 INFO::Removing potential empty rows and columns
2024-11-07 20:31:58.575095 INFO::Found 0 missing values.
2024-11-07 20:31:58.577709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:58.578202 INFO::Done
2024-11-07 20:31:58.578681 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:58.581463 INFO::Starting hierarchical adjustment
2024-11-07 20:31:58.582124 INFO::Found 2 batches.
2024-11-07 20:31:58.582603 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:58.583171 INFO::Using default BPPARAM
2024-11-07 20:31:58.583649 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:58.584495 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:58.598378 INFO::Done
2024-11-07 20:31:58.59895 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:58.601667 INFO::ASW Batch was 0.499670140526149 prior to batch effect correction and is now -0.00613586648565829 .
2024-11-07 20:31:58.602209 INFO::ASW Label was 0.564206481435545 prior to batch effect correction and is now 0.8987386318606 .
2024-11-07 20:31:58.602896 INFO::Total function execution time is 0.0302197933197021 s and adjustment time is 0.0163981914520264 s ( 54.26 )
2024-11-07 20:31:58.613834 INFO::Formatting Data.
2024-11-07 20:31:58.614468 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:58.615331 INFO::Removing potential empty rows and columns
2024-11-07 20:31:58.61619 INFO::Found 0 missing values.
2024-11-07 20:31:58.618152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:58.618648 INFO::Done
2024-11-07 20:31:58.619138 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:58.620857 INFO::Starting hierarchical adjustment
2024-11-07 20:31:58.621499 INFO::Found 2 batches.
2024-11-07 20:31:58.622002 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:58.622558 INFO::Using default BPPARAM
2024-11-07 20:31:58.623071 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:58.623904 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:58.654084 INFO::Done
2024-11-07 20:31:58.654708 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:58.656575 INFO::ASW Batch was 0.0520157260115974 prior to batch effect correction and is now -0.0536309624493463 .
2024-11-07 20:31:58.657346 INFO::Total function execution time is 0.0435492992401123 s and adjustment time is 0.0326905250549316 s ( 75.07 )
2024-11-07 20:31:58.668511 INFO::Formatting Data.
2024-11-07 20:31:58.669145 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:58.669956 INFO::Removing potential empty rows and columns
2024-11-07 20:31:58.670871 INFO::Found 0 missing values.
2024-11-07 20:31:58.671968 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 20:31:58.676312 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:58.676808 INFO::Done
2024-11-07 20:31:58.677277 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:58.680115 INFO::Starting hierarchical adjustment
2024-11-07 20:31:58.680814 INFO::Found 2 batches.
2024-11-07 20:31:58.681315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:58.681936 INFO::Using default BPPARAM
2024-11-07 20:31:58.682451 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:58.683374 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:58.699638 INFO::Done
2024-11-07 20:31:58.700234 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:58.703215 INFO::ASW Batch was 0.630519509369819 prior to batch effect correction and is now -0.0355787130162427 .
2024-11-07 20:31:58.703805 INFO::ASW Label was 0.388520101318042 prior to batch effect correction and is now 0.914530063739743 .
2024-11-07 20:31:58.704582 INFO::Total function execution time is 0.0361232757568359 s and adjustment time is 0.01896071434021 s ( 52.49 )
2024-11-07 20:31:58.705318 INFO::Formatting Data.
2024-11-07 20:31:58.705889 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:58.706725 INFO::Removing potential empty rows and columns
2024-11-07 20:31:58.707629 INFO::Found 0 missing values.
2024-11-07 20:31:58.708463 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 20:31:58.712654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:58.71315 INFO::Done
2024-11-07 20:31:58.713611 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:58.716269 INFO::Starting hierarchical adjustment
2024-11-07 20:31:58.716901 INFO::Found 2 batches.
2024-11-07 20:31:58.717378 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:58.717924 INFO::Using default BPPARAM
2024-11-07 20:31:58.718391 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:31:58.719217 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:31:58.734587 INFO::Done
2024-11-07 20:31:58.735154 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:58.737856 INFO::ASW Batch was 0.630519509369819 prior to batch effect correction and is now -0.0355787130162427 .
2024-11-07 20:31:58.738378 INFO::ASW Label was 0.388520101318042 prior to batch effect correction and is now 0.914530063739743 .
2024-11-07 20:31:58.739096 INFO::Total function execution time is 0.0337932109832764 s and adjustment time is 0.0178122520446777 s ( 52.71 )
2024-11-07 20:31:58.928427 INFO::Formatting Data.
2024-11-07 20:31:58.929162 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:58.930011 INFO::Removing potential empty rows and columns
2024-11-07 20:31:58.931033 INFO::Found 0 missing values.
2024-11-07 20:31:58.933977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:58.934501 INFO::Done
2024-11-07 20:31:58.935015 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:58.936962 INFO::Starting hierarchical adjustment
2024-11-07 20:31:58.937659 INFO::Found 3 batches.
2024-11-07 20:31:58.93822 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:58.938829 INFO::Using default BPPARAM
2024-11-07 20:31:58.939328 INFO::Processing subtree level 1
2024-11-07 20:31:59.06892 INFO::Adjusting the last 1 batches sequentially
2024-11-07 20:31:59.070542 INFO::Done
2024-11-07 20:31:59.071177 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:59.073565 INFO::ASW Batch was 0.00260499147235229 prior to batch effect correction and is now 0.00260499147235229 .
2024-11-07 20:31:59.074473 INFO::Total function execution time is 0.146084547042847 s and adjustment time is 0.133016347885132 s ( 91.05 )
2024-11-07 20:31:59.075564 INFO::Formatting Data.
2024-11-07 20:31:59.076236 INFO::Typecasting input to dataframe.
2024-11-07 20:31:59.077007 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:59.077899 INFO::Removing potential empty rows and columns
2024-11-07 20:31:59.078992 INFO::Found 0 missing values.
2024-11-07 20:31:59.086465 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:59.087366 INFO::Done
2024-11-07 20:31:59.087933 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:59.090453 INFO::Starting hierarchical adjustment
2024-11-07 20:31:59.091204 INFO::Found 3 batches.
2024-11-07 20:31:59.091752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:59.092422 INFO::Using default BPPARAM
2024-11-07 20:31:59.092963 INFO::Processing subtree level 1
2024-11-07 20:31:59.234488 INFO::Adjusting the last 1 batches sequentially
2024-11-07 20:31:59.236126 INFO::Done
2024-11-07 20:31:59.236731 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:59.23908 INFO::ASW Batch was 0.00260499147235229 prior to batch effect correction and is now 0.00260499147235229 .
2024-11-07 20:31:59.240044 INFO::Total function execution time is 0.164476156234741 s and adjustment time is 0.145090579986572 s ( 88.21 )
2024-11-07 20:31:59.253496 INFO::Formatting Data.
2024-11-07 20:31:59.254199 INFO::Typecasting input to dataframe.
2024-11-07 20:31:59.254995 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:59.255864 INFO::Removing potential empty rows and columns
2024-11-07 20:31:59.256907 INFO::Found 0 missing values.
2024-11-07 20:31:59.283279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:59.284448 INFO::Done
2024-11-07 20:31:59.284971 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:59.287034 INFO::Starting hierarchical adjustment
2024-11-07 20:31:59.287733 INFO::Found 3 batches.
2024-11-07 20:31:59.28824 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:59.288802 INFO::Using default BPPARAM
2024-11-07 20:31:59.28929 INFO::Processing subtree level 1
2024-11-07 20:31:59.393142 INFO::Adjusting the last 1 batches sequentially
2024-11-07 20:31:59.394813 INFO::Done
2024-11-07 20:31:59.395396 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:59.397797 INFO::ASW Batch was -0.0456814173010205 prior to batch effect correction and is now -0.0456814173010205 .
2024-11-07 20:31:59.398687 INFO::Total function execution time is 0.145211458206177 s and adjustment time is 0.107227325439453 s ( 73.84 )
2024-11-07 20:31:59.547127 INFO::Formatting Data.
2024-11-07 20:31:59.547826 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:59.548906 INFO::Removing potential empty rows and columns
2024-11-07 20:31:59.551638 INFO::Found 1000 missing values.
2024-11-07 20:31:59.569664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:59.570358 INFO::Done
2024-11-07 20:31:59.570863 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:59.575945 INFO::Starting hierarchical adjustment
2024-11-07 20:31:59.576625 INFO::Found 10 batches.
2024-11-07 20:31:59.577111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:31:59.577664 INFO::Using default BPPARAM
2024-11-07 20:31:59.578152 INFO::Processing subtree level 1
2024-11-07 20:31:59.745723 INFO::Processing subtree level 2
2024-11-07 20:31:59.926419 INFO::Adjusting the last 1 batches sequentially
2024-11-07 20:31:59.928394 INFO::Done
2024-11-07 20:31:59.92904 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:31:59.935039 INFO::ASW Batch was 0.49836891199205 prior to batch effect correction and is now 0.49836891199205 .
2024-11-07 20:31:59.935664 INFO::ASW Label was 0.3303957830935 prior to batch effect correction and is now 0.3303957830935 .
2024-11-07 20:31:59.93658 INFO::Total function execution time is 0.389458656311035 s and adjustment time is 0.351890802383423 s ( 90.35 )
2024-11-07 20:31:59.93746 INFO::Formatting Data.
2024-11-07 20:31:59.938165 INFO::Replacing NaNs with NAs.
2024-11-07 20:31:59.939617 INFO::Removing potential empty rows and columns
2024-11-07 20:31:59.942536 INFO::Found 1000 missing values.
2024-11-07 20:31:59.962745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:31:59.963408 INFO::Done
2024-11-07 20:31:59.963978 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:31:59.969804 INFO::Starting hierarchical adjustment
2024-11-07 20:31:59.970588 INFO::Found 10 batches.
2024-11-07 20:32:00.996953 INFO::Set up parallel execution backend with 2 workers
2024-11-07 20:32:00.998274 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-11-07 20:32:01.980078 INFO::Adjusting the last 2 batches sequentially
2024-11-07 20:32:01.981424 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 20:32:01.996716 INFO::Done
2024-11-07 20:32:01.997285 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:32:02.001667 INFO::ASW Batch was 0.49836891199205 prior to batch effect correction and is now 0.49836891199205 .
2024-11-07 20:32:02.002193 INFO::ASW Label was 0.3303957830935 prior to batch effect correction and is now 0.3303957830935 .
2024-11-07 20:32:02.002864 INFO::Total function execution time is 2.06544542312622 s and adjustment time is 2.02629065513611 s ( 98.1 )
2024-11-07 20:32:02.144411 INFO::Formatting Data.
2024-11-07 20:32:02.145274 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.1462 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.147325 INFO::Found 0 missing values.
2024-11-07 20:32:02.151127 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.151629 INFO::Done
2024-11-07 20:32:02.152137 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 20:32:02.154907 INFO::Starting hierarchical adjustment
2024-11-07 20:32:02.15597 INFO::Found 3 batches.
2024-11-07 20:32:02.156447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 20:32:02.157029 INFO::Using default BPPARAM
2024-11-07 20:32:02.157501 INFO::Processing subtree level 1
2024-11-07 20:32:02.259186 INFO::Adjusting the last 1 batches sequentially
2024-11-07 20:32:02.260789 INFO::Done
2024-11-07 20:32:02.261371 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 20:32:02.264317 INFO::ASW Batch was 0.318690680014704 prior to batch effect correction and is now -0.172672489387052 .
2024-11-07 20:32:02.264903 INFO::ASW Label was -0.191426828210941 prior to batch effect correction and is now 0.00945036001967723 .
2024-11-07 20:32:02.265728 INFO::Total function execution time is 0.121383905410767 s and adjustment time is 0.104934453964233 s ( 86.45 )
2024-11-07 20:32:02.369313 INFO::Formatting Data.
2024-11-07 20:32:02.370057 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.370857 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.371799 INFO::Found 2 missing values.
2024-11-07 20:32:02.374365 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.374856 INFO::Done
2024-11-07 20:32:02.398935 INFO::Found NA in Reference column
2024-11-07 20:32:02.407535 INFO::Require at least two references per batch.
2024-11-07 20:32:02.425935 INFO::Formatting Data.
2024-11-07 20:32:02.426565 INFO::Recognized SummarizedExperiment
2024-11-07 20:32:02.42705 INFO::Typecasting input to dataframe.
2024-11-07 20:32:02.435831 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.436801 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.440037 INFO::Found 0 missing values.
2024-11-07 20:32:02.44621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.446732 INFO::Done
2024-11-07 20:32:02.460434 INFO::Formatting Data.
2024-11-07 20:32:02.461052 INFO::Recognized SummarizedExperiment
2024-11-07 20:32:02.461505 INFO::Typecasting input to dataframe.
2024-11-07 20:32:02.477219 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.478269 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.481506 INFO::Found 0 missing values.
2024-11-07 20:32:02.491692 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.492246 INFO::Done
2024-11-07 20:32:02.506297 INFO::Formatting Data.
2024-11-07 20:32:02.506923 INFO::Recognized SummarizedExperiment
2024-11-07 20:32:02.507386 INFO::Typecasting input to dataframe.
2024-11-07 20:32:02.522524 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.523407 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.524391 INFO::Found 0 missing values.
2024-11-07 20:32:02.525238 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 20:32:02.529433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.529937 INFO::Done
2024-11-07 20:32:02.538996 INFO::Formatting Data.
2024-11-07 20:32:02.539607 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.540419 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.54165 INFO::Found 0 missing values.
2024-11-07 20:32:02.552818 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.553507 INFO::Done
2024-11-07 20:32:02.564901 INFO::Formatting Data.
2024-11-07 20:32:02.565587 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.566415 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.567431 INFO::Found 0 missing values.
2024-11-07 20:32:02.570333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.570844 INFO::Done
2024-11-07 20:32:02.599035 INFO::Formatting Data.
2024-11-07 20:32:02.599796 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.600929 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.602198 INFO::Found 1 missing values.
2024-11-07 20:32:02.604707 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.605211 INFO::Done
2024-11-07 20:32:02.623177 INFO::Formatting Data.
2024-11-07 20:32:02.623904 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.624711 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.625603 INFO::Found 2 missing values.
2024-11-07 20:32:02.626505 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 20:32:02.628831 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.62935 INFO::Done
2024-11-07 20:32:02.639289 INFO::Formatting Data.
2024-11-07 20:32:02.639979 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.640844 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.641782 INFO::Found 2 missing values.
2024-11-07 20:32:02.64341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.643914 INFO::Done
2024-11-07 20:32:02.654446 INFO::Formatting Data.
2024-11-07 20:32:02.655091 INFO::Typecasting input to dataframe.
2024-11-07 20:32:02.65591 INFO::Replacing NaNs with NAs.
2024-11-07 20:32:02.656715 INFO::Removing potential empty rows and columns
2024-11-07 20:32:02.657719 INFO::Found 0 missing values.
2024-11-07 20:32:02.660671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 20:32:02.661227 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
14.868 3.601 18.055
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 21.239 | 1.340 | 15.608 | |
| compute_asw | 0.023 | 0.000 | 0.022 | |
| count_existing | 0.012 | 0.001 | 0.013 | |
| generate_data_covariables | 0.011 | 0.000 | 0.011 | |
| generate_dataset | 0.011 | 0.000 | 0.011 | |