Yannis Schumann
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 10fd252 |
| git_last_commit_date: 2024-11-20 10:26:09 -0500 (Wed, 20 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:39 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 159/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.3 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.3.3 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.3.tar.gz |
| StartedAt: 2025-01-03 20:01:25 -0500 (Fri, 03 Jan 2025) |
| EndedAt: 2025-01-03 20:02:55 -0500 (Fri, 03 Jan 2025) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BERT.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘1.3.3’
* 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 ... WARNING
Undocumented code objects:
‘generate_truncated_dataset’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 25.105 1.417 18.243
* 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: 1 WARNING
See
‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck/00check.log’
for details.
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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) (2024-10-21 r87258) -- "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")
2025-01-03 20:02:17.605917 INFO::Formatting Data.
2025-01-03 20:02:17.607582 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:17.620314 INFO::Removing potential empty rows and columns
2025-01-03 20:02:17.872187 INFO::Found 0 missing values.
2025-01-03 20:02:17.875916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:17.876711 INFO::Done
2025-01-03 20:02:17.8773 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:17.890348 INFO::Starting hierarchical adjustment
2025-01-03 20:02:17.89151 INFO::Found 3 batches.
2025-01-03 20:02:17.892155 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:17.893557 INFO::Using default BPPARAM
2025-01-03 20:02:17.894145 INFO::Processing subtree level 1
2025-01-03 20:02:18.003107 INFO::Adjusting the last 1 batches sequentially
2025-01-03 20:02:18.005097 INFO::Done
2025-01-03 20:02:18.005862 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:18.008682 INFO::ASW Batch was 0.0413636410767534 prior to batch effect correction and is now 0.0413636410767534 .
2025-01-03 20:02:18.009907 INFO::Total function execution time is 0.404740333557129 s and adjustment time is 0.113843679428101 s ( 28.13 )
2025-01-03 20:02:18.024251 INFO::Formatting Data.
2025-01-03 20:02:18.025114 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:18.026126 INFO::Removing potential empty rows and columns
2025-01-03 20:02:18.027271 INFO::Found 0 missing values.
2025-01-03 20:02:18.028275 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.
2025-01-03 20:02:18.039413 INFO::Formatting Data.
2025-01-03 20:02:18.040262 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:18.04124 INFO::Removing potential empty rows and columns
2025-01-03 20:02:18.042314 INFO::Found 0 missing values.
2025-01-03 20:02:18.043269 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.
2025-01-03 20:02:18.059191 INFO::Formatting Data.
2025-01-03 20:02:18.059937 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:18.060833 INFO::Removing potential empty rows and columns
2025-01-03 20:02:18.061848 INFO::Found 0 missing values.
2025-01-03 20:02:18.062752 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.
2025-01-03 20:02:18.067163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:18.067715 INFO::Done
2025-01-03 20:02:18.068245 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:18.070283 INFO::Starting hierarchical adjustment
2025-01-03 20:02:18.070996 INFO::Found 2 batches.
2025-01-03 20:02:18.07151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:18.072164 INFO::Using default BPPARAM
2025-01-03 20:02:18.072711 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:18.083568 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:18.109675 INFO::Done
2025-01-03 20:02:18.110523 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:18.113191 INFO::ASW Batch was -0.0140181724673056 prior to batch effect correction and is now -0.12772561261457 .
2025-01-03 20:02:18.114149 INFO::Total function execution time is 0.0549919605255127 s and adjustment time is 0.0387704372406006 s ( 70.5 )
2025-01-03 20:02:18.117851 INFO::Formatting Data.
2025-01-03 20:02:18.118557 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:18.128383 INFO::Formatting Data.
2025-01-03 20:02:18.129228 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:18.13021 INFO::Removing potential empty rows and columns
2025-01-03 20:02:18.131363 INFO::Found 0 missing values.
2025-01-03 20:02:18.134486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:18.135039 INFO::Done
2025-01-03 20:02:18.135581 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:18.137811 INFO::Starting hierarchical adjustment
2025-01-03 20:02:18.138557 INFO::Found 2 batches.
2025-01-03 20:02:18.182662 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:18.185644 INFO::Using default BPPARAM
2025-01-03 20:02:18.186283 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:18.187337 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:18.202836 INFO::Done
2025-01-03 20:02:18.203589 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:18.205742 INFO::ASW Batch was -0.0224548757791294 prior to batch effect correction and is now -0.123384039891309 .
2025-01-03 20:02:18.206581 INFO::Total function execution time is 0.0783069133758545 s and adjustment time is 0.064417839050293 s ( 82.26 )
2025-01-03 20:02:18.207696 INFO::Formatting Data.
2025-01-03 20:02:18.208303 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:18.209172 INFO::Removing potential empty rows and columns
2025-01-03 20:02:18.210187 INFO::Found 0 missing values.
2025-01-03 20:02:18.213079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:18.213615 INFO::Done
2025-01-03 20:02:18.214141 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:18.216249 INFO::Starting hierarchical adjustment
2025-01-03 20:02:18.216943 INFO::Found 2 batches.
2025-01-03 20:02:18.217467 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:18.218062 INFO::Using default BPPARAM
2025-01-03 20:02:18.218576 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:18.219489 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:18.235558 INFO::Done
2025-01-03 20:02:18.236293 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:18.23835 INFO::ASW Batch was -0.0224548757791294 prior to batch effect correction and is now -0.123384039891309 .
2025-01-03 20:02:18.239176 INFO::Total function execution time is 0.031498908996582 s and adjustment time is 0.0187258720397949 s ( 59.45 )
2025-01-03 20:02:21.21411 INFO::Formatting Data.
2025-01-03 20:02:21.214836 INFO::Recognized SummarizedExperiment
2025-01-03 20:02:21.215342 INFO::Typecasting input to dataframe.
2025-01-03 20:02:21.243191 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:21.24436 INFO::Removing potential empty rows and columns
2025-01-03 20:02:21.24752 INFO::Found 0 missing values.
2025-01-03 20:02:21.253368 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:21.253925 INFO::Done
2025-01-03 20:02:21.254399 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:21.257707 INFO::Starting hierarchical adjustment
2025-01-03 20:02:21.258418 INFO::Found 2 batches.
2025-01-03 20:02:21.258912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:21.25993 INFO::Using default BPPARAM
2025-01-03 20:02:21.260444 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:21.261375 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:21.316323 INFO::Done
2025-01-03 20:02:21.317061 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:21.320609 INFO::ASW Batch was 0.00820136666278768 prior to batch effect correction and is now -0.0976432826881426 .
2025-01-03 20:02:21.321453 INFO::Total function execution time is 0.107595682144165 s and adjustment time is 0.0580217838287354 s ( 53.93 )
2025-01-03 20:02:21.340603 INFO::Formatting Data.
2025-01-03 20:02:21.341413 INFO::Recognized SummarizedExperiment
2025-01-03 20:02:21.341993 INFO::Typecasting input to dataframe.
2025-01-03 20:02:21.351368 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:21.352576 INFO::Removing potential empty rows and columns
2025-01-03 20:02:21.356383 INFO::Found 0 missing values.
2025-01-03 20:02:21.363471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:21.364078 INFO::Done
2025-01-03 20:02:21.364622 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:21.368047 INFO::Starting hierarchical adjustment
2025-01-03 20:02:21.368779 INFO::Found 2 batches.
2025-01-03 20:02:21.369294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:21.369876 INFO::Using default BPPARAM
2025-01-03 20:02:21.370407 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:21.371353 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:21.395922 INFO::Done
2025-01-03 20:02:21.396626 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:21.400095 INFO::ASW Batch was -0.0171106723355406 prior to batch effect correction and is now -0.0171106723355406 .
2025-01-03 20:02:21.400938 INFO::Total function execution time is 0.0603289604187012 s and adjustment time is 0.0272641181945801 s ( 45.19 )
2025-01-03 20:02:21.418453 INFO::Formatting Data.
2025-01-03 20:02:21.419207 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:21.42008 INFO::Removing potential empty rows and columns
2025-01-03 20:02:21.421107 INFO::Found 0 missing values.
2025-01-03 20:02:21.424012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:21.42454 INFO::Done
2025-01-03 20:02:21.425044 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:21.426991 INFO::Starting hierarchical adjustment
2025-01-03 20:02:21.427677 INFO::Found 3 batches.
2025-01-03 20:02:21.42818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:21.428793 INFO::Using default BPPARAM
2025-01-03 20:02:21.429314 INFO::Processing subtree level 1
2025-01-03 20:02:21.569468 INFO::Adjusting the last 1 batches sequentially
2025-01-03 20:02:21.571566 INFO::Done
2025-01-03 20:02:21.572366 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:21.57515 INFO::ASW Batch was -0.00689892263878813 prior to batch effect correction and is now -0.161872138177675 .
2025-01-03 20:02:21.576236 INFO::Total function execution time is 0.157763719558716 s and adjustment time is 0.143981456756592 s ( 91.26 )
2025-01-03 20:02:21.591888 INFO::Skipping initial DF formatting
2025-01-03 20:02:21.592725 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:21.597667 INFO::Starting hierarchical adjustment
2025-01-03 20:02:21.598728 INFO::Found 5 batches.
2025-01-03 20:02:21.599387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:21.600153 INFO::Using default BPPARAM
2025-01-03 20:02:21.600778 INFO::Processing subtree level 1
2025-01-03 20:02:21.743114 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:21.745517 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:21.766694 INFO::Done
2025-01-03 20:02:21.767429 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:21.772075 INFO::ASW Batch was 0.407619025910756 prior to batch effect correction and is now 0.407619025910756 .
2025-01-03 20:02:21.772841 INFO::ASW Label was 0.459583556957782 prior to batch effect correction and is now 0.459583556957782 .
2025-01-03 20:02:21.773944 INFO::Total function execution time is 0.182165145874023 s and adjustment time is 0.168210506439209 s ( 92.34 )
2025-01-03 20:02:21.793504 INFO::Formatting Data.
2025-01-03 20:02:21.794344 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:21.795348 INFO::Removing potential empty rows and columns
2025-01-03 20:02:21.796392 INFO::Found 0 missing values.
2025-01-03 20:02:21.800564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:21.801137 INFO::Done
2025-01-03 20:02:21.801679 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:21.804783 INFO::Starting hierarchical adjustment
2025-01-03 20:02:21.805532 INFO::Found 5 batches.
2025-01-03 20:02:21.806045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:21.806763 INFO::Using default BPPARAM
2025-01-03 20:02:21.8073 INFO::Processing subtree level 1
2025-01-03 20:02:21.923612 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:21.925612 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:21.943601 INFO::Done
2025-01-03 20:02:21.944578 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:21.948272 INFO::ASW Batch was 0.590920552123273 prior to batch effect correction and is now -0.095435351680144 .
2025-01-03 20:02:21.949023 INFO::ASW Label was 0.150750693317685 prior to batch effect correction and is now 0.839798092392995 .
2025-01-03 20:02:21.949966 INFO::Total function execution time is 0.156531810760498 s and adjustment time is 0.138134002685547 s ( 88.25 )
2025-01-03 20:02:21.950915 INFO::Formatting Data.
2025-01-03 20:02:21.95157 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:21.952531 INFO::Removing potential empty rows and columns
2025-01-03 20:02:21.953609 INFO::Found 0 missing values.
2025-01-03 20:02:21.957915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:21.958507 INFO::Done
2025-01-03 20:02:21.959025 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:21.962241 INFO::Starting hierarchical adjustment
2025-01-03 20:02:21.962986 INFO::Found 5 batches.
2025-01-03 20:02:21.963548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:21.96422 INFO::Using default BPPARAM
2025-01-03 20:02:21.964792 INFO::Processing subtree level 1
2025-01-03 20:02:22.09258 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:22.09459 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:22.111911 INFO::Done
2025-01-03 20:02:22.112787 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:22.116413 INFO::ASW Batch was 0.590920552123273 prior to batch effect correction and is now -0.095435351680144 .
2025-01-03 20:02:22.117223 INFO::ASW Label was 0.150750693317685 prior to batch effect correction and is now 0.839798092392995 .
2025-01-03 20:02:22.118186 INFO::Total function execution time is 0.16731858253479 s and adjustment time is 0.149004220962524 s ( 89.05 )
2025-01-03 20:02:22.133133 INFO::Formatting Data.
2025-01-03 20:02:22.134052 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:22.135114 INFO::Removing potential empty rows and columns
2025-01-03 20:02:22.136232 INFO::Found 0 missing values.
2025-01-03 20:02:22.140583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:22.141231 INFO::Done
2025-01-03 20:02:22.141781 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:22.145112 INFO::Starting hierarchical adjustment
2025-01-03 20:02:22.145913 INFO::Found 5 batches.
2025-01-03 20:02:22.14648 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:22.147142 INFO::Using default BPPARAM
2025-01-03 20:02:22.147686 INFO::Processing subtree level 1
2025-01-03 20:02:22.275008 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:22.276996 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:22.294995 INFO::Done
2025-01-03 20:02:22.29607 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:22.300065 INFO::ASW Batch was 0.410815624743067 prior to batch effect correction and is now 0.0098441020574432 .
2025-01-03 20:02:22.300907 INFO::ASW Label was 0.464356362115466 prior to batch effect correction and is now 0.737401665189479 .
2025-01-03 20:02:22.301919 INFO::Total function execution time is 0.16888427734375 s and adjustment time is 0.149146556854248 s ( 88.31 )
2025-01-03 20:02:22.302951 INFO::Formatting Data.
2025-01-03 20:02:22.303651 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:22.304731 INFO::Removing potential empty rows and columns
2025-01-03 20:02:22.305855 INFO::Found 0 missing values.
2025-01-03 20:02:22.310351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:22.310933 INFO::Done
2025-01-03 20:02:22.311466 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:22.314921 INFO::Starting hierarchical adjustment
2025-01-03 20:02:22.315729 INFO::Found 5 batches.
2025-01-03 20:02:22.3163 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:22.317104 INFO::Using default BPPARAM
2025-01-03 20:02:22.317671 INFO::Processing subtree level 1
2025-01-03 20:02:22.452429 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:22.45476 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:22.47721 INFO::Done
2025-01-03 20:02:22.478405 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:22.495549 INFO::ASW Batch was 0.410815624743067 prior to batch effect correction and is now 0.0098441020574432 .
2025-01-03 20:02:22.496556 INFO::ASW Label was 0.464356362115466 prior to batch effect correction and is now 0.737401665189479 .
2025-01-03 20:02:22.497585 INFO::Total function execution time is 0.194656372070312 s and adjustment time is 0.161547183990479 s ( 82.99 )
2025-01-03 20:02:22.513017 INFO::Formatting Data.
2025-01-03 20:02:22.513912 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:22.514967 INFO::Removing potential empty rows and columns
2025-01-03 20:02:22.516099 INFO::Found 0 missing values.
2025-01-03 20:02:22.519176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:22.519759 INFO::Done
2025-01-03 20:02:22.520293 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:22.523473 INFO::Starting hierarchical adjustment
2025-01-03 20:02:22.524316 INFO::Found 2 batches.
2025-01-03 20:02:22.524874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:22.525613 INFO::Using default BPPARAM
2025-01-03 20:02:22.526155 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:22.527144 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:22.543781 INFO::Done
2025-01-03 20:02:22.54453 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:22.54774 INFO::ASW Batch was 0.583098698940573 prior to batch effect correction and is now -0.0255760025503842 .
2025-01-03 20:02:22.548394 INFO::ASW Label was 0.466968963840531 prior to batch effect correction and is now 0.920937566768426 .
2025-01-03 20:02:22.549284 INFO::Total function execution time is 0.0363893508911133 s and adjustment time is 0.0196590423583984 s ( 54.02 )
2025-01-03 20:02:22.550128 INFO::Formatting Data.
2025-01-03 20:02:22.550766 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:22.551676 INFO::Removing potential empty rows and columns
2025-01-03 20:02:22.55269 INFO::Found 0 missing values.
2025-01-03 20:02:22.637437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:22.63931 INFO::Done
2025-01-03 20:02:22.639987 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:22.643391 INFO::Starting hierarchical adjustment
2025-01-03 20:02:22.644251 INFO::Found 2 batches.
2025-01-03 20:02:22.644821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:22.645496 INFO::Using default BPPARAM
2025-01-03 20:02:22.646095 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:22.647155 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:22.664992 INFO::Done
2025-01-03 20:02:22.66577 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:22.669111 INFO::ASW Batch was 0.583098698940573 prior to batch effect correction and is now -0.0255760025503842 .
2025-01-03 20:02:22.669764 INFO::ASW Label was 0.466968963840531 prior to batch effect correction and is now 0.920937566768426 .
2025-01-03 20:02:22.670629 INFO::Total function execution time is 0.120516538619995 s and adjustment time is 0.0209088325500488 s ( 17.35 )
2025-01-03 20:02:22.68284 INFO::Formatting Data.
2025-01-03 20:02:22.683643 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:22.684546 INFO::Removing potential empty rows and columns
2025-01-03 20:02:22.685463 INFO::Found 0 missing values.
2025-01-03 20:02:22.687549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:22.688108 INFO::Done
2025-01-03 20:02:22.688656 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:22.690564 INFO::Starting hierarchical adjustment
2025-01-03 20:02:22.6913 INFO::Found 2 batches.
2025-01-03 20:02:22.691818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:22.692446 INFO::Using default BPPARAM
2025-01-03 20:02:22.692961 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:22.693909 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:22.727644 INFO::Done
2025-01-03 20:02:22.728378 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:22.73041 INFO::ASW Batch was -0.140909217859473 prior to batch effect correction and is now -0.171423139852808 .
2025-01-03 20:02:22.731261 INFO::Total function execution time is 0.0484957695007324 s and adjustment time is 0.0364906787872314 s ( 75.25 )
2025-01-03 20:02:22.743741 INFO::Formatting Data.
2025-01-03 20:02:22.744614 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:22.74555 INFO::Removing potential empty rows and columns
2025-01-03 20:02:22.746589 INFO::Found 0 missing values.
2025-01-03 20:02:22.747739 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.
2025-01-03 20:02:22.752433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:22.753027 INFO::Done
2025-01-03 20:02:22.753565 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:22.756603 INFO::Starting hierarchical adjustment
2025-01-03 20:02:22.757316 INFO::Found 2 batches.
2025-01-03 20:02:22.757863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:22.758498 INFO::Using default BPPARAM
2025-01-03 20:02:22.759031 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:22.760124 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:22.777941 INFO::Done
2025-01-03 20:02:22.778703 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:22.781939 INFO::ASW Batch was 0.637172775750034 prior to batch effect correction and is now 0.0040335045557547 .
2025-01-03 20:02:22.782566 INFO::ASW Label was 0.471347388502373 prior to batch effect correction and is now 0.937417944231123 .
2025-01-03 20:02:22.783508 INFO::Total function execution time is 0.0398521423339844 s and adjustment time is 0.0207633972167969 s ( 52.1 )
2025-01-03 20:02:22.784455 INFO::Formatting Data.
2025-01-03 20:02:22.785094 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:22.786075 INFO::Removing potential empty rows and columns
2025-01-03 20:02:22.787187 INFO::Found 0 missing values.
2025-01-03 20:02:22.78827 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.
2025-01-03 20:02:22.792926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:22.793515 INFO::Done
2025-01-03 20:02:22.794065 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:22.797006 INFO::Starting hierarchical adjustment
2025-01-03 20:02:22.797711 INFO::Found 2 batches.
2025-01-03 20:02:22.798247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:22.798872 INFO::Using default BPPARAM
2025-01-03 20:02:22.799392 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:22.800332 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:22.818147 INFO::Done
2025-01-03 20:02:22.818895 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:22.822192 INFO::ASW Batch was 0.637172775750034 prior to batch effect correction and is now 0.0040335045557547 .
2025-01-03 20:02:22.822966 INFO::ASW Label was 0.471347388502373 prior to batch effect correction and is now 0.937417944231123 .
2025-01-03 20:02:22.823949 INFO::Total function execution time is 0.039496898651123 s and adjustment time is 0.02054762840271 s ( 52.02 )
2025-01-03 20:02:23.031176 INFO::Formatting Data.
2025-01-03 20:02:23.031971 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:23.032877 INFO::Removing potential empty rows and columns
2025-01-03 20:02:23.033903 INFO::Found 0 missing values.
2025-01-03 20:02:23.036795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:23.037344 INFO::Done
2025-01-03 20:02:23.03785 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:23.039767 INFO::Starting hierarchical adjustment
2025-01-03 20:02:23.040452 INFO::Found 3 batches.
2025-01-03 20:02:23.040951 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:23.041558 INFO::Using default BPPARAM
2025-01-03 20:02:23.042058 INFO::Processing subtree level 1
2025-01-03 20:02:23.140643 INFO::Adjusting the last 1 batches sequentially
2025-01-03 20:02:23.142674 INFO::Done
2025-01-03 20:02:23.143436 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:23.146256 INFO::ASW Batch was -0.0776278069704565 prior to batch effect correction and is now -0.0776278069704565 .
2025-01-03 20:02:23.147336 INFO::Total function execution time is 0.116157531738281 s and adjustment time is 0.102300643920898 s ( 88.07 )
2025-01-03 20:02:23.148581 INFO::Formatting Data.
2025-01-03 20:02:23.149312 INFO::Typecasting input to dataframe.
2025-01-03 20:02:23.150144 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:23.151245 INFO::Removing potential empty rows and columns
2025-01-03 20:02:23.15255 INFO::Found 0 missing values.
2025-01-03 20:02:23.155822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:23.156453 INFO::Done
2025-01-03 20:02:23.157071 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:23.159401 INFO::Starting hierarchical adjustment
2025-01-03 20:02:23.160171 INFO::Found 3 batches.
2025-01-03 20:02:23.160746 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:23.16143 INFO::Using default BPPARAM
2025-01-03 20:02:23.162014 INFO::Processing subtree level 1
2025-01-03 20:02:23.269794 INFO::Adjusting the last 1 batches sequentially
2025-01-03 20:02:23.271957 INFO::Done
2025-01-03 20:02:23.272692 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:23.275522 INFO::ASW Batch was -0.0776278069704565 prior to batch effect correction and is now -0.0776278069704565 .
2025-01-03 20:02:23.276606 INFO::Total function execution time is 0.128009796142578 s and adjustment time is 0.111924648284912 s ( 87.43 )
2025-01-03 20:02:23.290612 INFO::Formatting Data.
2025-01-03 20:02:23.291476 INFO::Typecasting input to dataframe.
2025-01-03 20:02:23.292421 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:23.293404 INFO::Removing potential empty rows and columns
2025-01-03 20:02:23.294538 INFO::Found 0 missing values.
2025-01-03 20:02:23.297557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:23.29811 INFO::Done
2025-01-03 20:02:23.298653 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:23.300705 INFO::Starting hierarchical adjustment
2025-01-03 20:02:23.301467 INFO::Found 3 batches.
2025-01-03 20:02:23.302033 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:23.302718 INFO::Using default BPPARAM
2025-01-03 20:02:23.303272 INFO::Processing subtree level 1
2025-01-03 20:02:23.405958 INFO::Adjusting the last 1 batches sequentially
2025-01-03 20:02:23.408506 INFO::Done
2025-01-03 20:02:23.409544 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:23.413024 INFO::ASW Batch was 0.0900984224080827 prior to batch effect correction and is now 0.0900984224080827 .
2025-01-03 20:02:23.414305 INFO::Total function execution time is 0.123672246932983 s and adjustment time is 0.107100009918213 s ( 86.6 )
2025-01-03 20:02:23.577411 INFO::Formatting Data.
2025-01-03 20:02:23.578259 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:23.57941 INFO::Removing potential empty rows and columns
2025-01-03 20:02:23.582181 INFO::Found 1000 missing values.
2025-01-03 20:02:23.601712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:23.602544 INFO::Done
2025-01-03 20:02:23.603159 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:23.608756 INFO::Starting hierarchical adjustment
2025-01-03 20:02:23.609579 INFO::Found 10 batches.
2025-01-03 20:02:23.610173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:23.610888 INFO::Using default BPPARAM
2025-01-03 20:02:23.611485 INFO::Processing subtree level 1
2025-01-03 20:02:23.771255 INFO::Processing subtree level 2
2025-01-03 20:02:23.940092 INFO::Adjusting the last 1 batches sequentially
2025-01-03 20:02:23.94224 INFO::Done
2025-01-03 20:02:23.942933 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:23.948648 INFO::ASW Batch was 0.524591985972399 prior to batch effect correction and is now 0.524591985972399 .
2025-01-03 20:02:23.949404 INFO::ASW Label was 0.318146633675709 prior to batch effect correction and is now 0.318146633675708 .
2025-01-03 20:02:23.950393 INFO::Total function execution time is 0.373021364212036 s and adjustment time is 0.332798480987549 s ( 89.22 )
2025-01-03 20:02:23.951329 INFO::Formatting Data.
2025-01-03 20:02:23.95204 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:23.953408 INFO::Removing potential empty rows and columns
2025-01-03 20:02:23.956191 INFO::Found 1000 missing values.
2025-01-03 20:02:23.975422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:23.976228 INFO::Done
2025-01-03 20:02:23.97682 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:23.982403 INFO::Starting hierarchical adjustment
2025-01-03 20:02:23.983226 INFO::Found 10 batches.
2025-01-03 20:02:25.265538 INFO::Set up parallel execution backend with 2 workers
2025-01-03 20:02:25.268077 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-03 20:02:26.514317 INFO::Adjusting the last 2 batches sequentially
2025-01-03 20:02:26.516009 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-03 20:02:26.531729 INFO::Done
2025-01-03 20:02:26.532324 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:26.536616 INFO::ASW Batch was 0.524591985972399 prior to batch effect correction and is now 0.524591985972399 .
2025-01-03 20:02:26.537128 INFO::ASW Label was 0.318146633675709 prior to batch effect correction and is now 0.318146633675708 .
2025-01-03 20:02:26.537871 INFO::Total function execution time is 2.5866105556488 s and adjustment time is 2.54869318008423 s ( 98.53 )
2025-01-03 20:02:26.688655 INFO::Formatting Data.
2025-01-03 20:02:26.689458 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:26.690333 INFO::Removing potential empty rows and columns
2025-01-03 20:02:26.691352 INFO::Found 0 missing values.
2025-01-03 20:02:26.694813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:26.695364 INFO::Done
2025-01-03 20:02:26.695857 INFO::Acquiring quality metrics before batch effect correction.
2025-01-03 20:02:26.698392 INFO::Starting hierarchical adjustment
2025-01-03 20:02:26.69905 INFO::Found 3 batches.
2025-01-03 20:02:26.699555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-03 20:02:26.700129 INFO::Using default BPPARAM
2025-01-03 20:02:26.700634 INFO::Processing subtree level 1
2025-01-03 20:02:26.807947 INFO::Adjusting the last 1 batches sequentially
2025-01-03 20:02:26.809706 INFO::Done
2025-01-03 20:02:26.810344 INFO::Acquiring quality metrics after batch effect correction.
2025-01-03 20:02:26.813655 INFO::ASW Batch was 0.169914465211998 prior to batch effect correction and is now -0.157794863946345 .
2025-01-03 20:02:26.81436 INFO::ASW Label was -0.167114144570315 prior to batch effect correction and is now 0.0255208709088294 .
2025-01-03 20:02:26.815291 INFO::Total function execution time is 0.126639604568481 s and adjustment time is 0.110760927200317 s ( 87.46 )
2025-01-03 20:02:26.923784 INFO::Formatting Data.
2025-01-03 20:02:26.924565 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:26.925436 INFO::Removing potential empty rows and columns
2025-01-03 20:02:26.926421 INFO::Found 2 missing values.
2025-01-03 20:02:26.92908 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:26.929607 INFO::Done
2025-01-03 20:02:26.954676 INFO::Found NA in Reference column
2025-01-03 20:02:26.963233 INFO::Require at least two references per batch.
2025-01-03 20:02:26.981714 INFO::Formatting Data.
2025-01-03 20:02:26.982444 INFO::Recognized SummarizedExperiment
2025-01-03 20:02:26.982972 INFO::Typecasting input to dataframe.
2025-01-03 20:02:26.992126 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:26.993253 INFO::Removing potential empty rows and columns
2025-01-03 20:02:26.996557 INFO::Found 0 missing values.
2025-01-03 20:02:27.002894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:27.00347 INFO::Done
2025-01-03 20:02:27.017337 INFO::Formatting Data.
2025-01-03 20:02:27.017982 INFO::Recognized SummarizedExperiment
2025-01-03 20:02:27.018487 INFO::Typecasting input to dataframe.
2025-01-03 20:02:27.034661 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:27.035796 INFO::Removing potential empty rows and columns
2025-01-03 20:02:27.039137 INFO::Found 0 missing values.
2025-01-03 20:02:27.049291 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:27.049875 INFO::Done
2025-01-03 20:02:27.063882 INFO::Formatting Data.
2025-01-03 20:02:27.064542 INFO::Recognized SummarizedExperiment
2025-01-03 20:02:27.065033 INFO::Typecasting input to dataframe.
2025-01-03 20:02:27.080704 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:27.081668 INFO::Removing potential empty rows and columns
2025-01-03 20:02:27.082693 INFO::Found 0 missing values.
2025-01-03 20:02:27.083578 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.
2025-01-03 20:02:27.087666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:27.088166 INFO::Done
2025-01-03 20:02:27.097396 INFO::Formatting Data.
2025-01-03 20:02:27.098056 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:27.098859 INFO::Removing potential empty rows and columns
2025-01-03 20:02:27.099806 INFO::Found 0 missing values.
2025-01-03 20:02:27.102445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:27.102938 INFO::Done
2025-01-03 20:02:27.113344 INFO::Formatting Data.
2025-01-03 20:02:27.11406 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:27.114888 INFO::Removing potential empty rows and columns
2025-01-03 20:02:27.115826 INFO::Found 0 missing values.
2025-01-03 20:02:27.118518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:27.119044 INFO::Done
2025-01-03 20:02:27.146534 INFO::Formatting Data.
2025-01-03 20:02:27.147354 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:27.148394 INFO::Removing potential empty rows and columns
2025-01-03 20:02:27.149531 INFO::Found 1 missing values.
2025-01-03 20:02:27.152032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:27.152562 INFO::Done
2025-01-03 20:02:27.170163 INFO::Formatting Data.
2025-01-03 20:02:27.170961 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:27.171854 INFO::Removing potential empty rows and columns
2025-01-03 20:02:27.172774 INFO::Found 2 missing values.
2025-01-03 20:02:27.173647 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.
2025-01-03 20:02:27.175785 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:27.176331 INFO::Done
2025-01-03 20:02:27.186121 INFO::Formatting Data.
2025-01-03 20:02:27.18685 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:27.187716 INFO::Removing potential empty rows and columns
2025-01-03 20:02:27.188598 INFO::Found 2 missing values.
2025-01-03 20:02:27.19012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:27.190622 INFO::Done
2025-01-03 20:02:27.200348 INFO::Formatting Data.
2025-01-03 20:02:27.201105 INFO::Typecasting input to dataframe.
2025-01-03 20:02:27.201879 INFO::Replacing NaNs with NAs.
2025-01-03 20:02:27.202695 INFO::Removing potential empty rows and columns
2025-01-03 20:02:27.203657 INFO::Found 0 missing values.
2025-01-03 20:02:27.206348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-03 20:02:27.206867 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 138 ]
>
> proc.time()
user system elapsed
17.479 3.944 21.140
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.105 | 1.417 | 18.243 | |
| compute_asw | 0.022 | 0.002 | 0.024 | |
| count_existing | 0.012 | 0.002 | 0.014 | |
| generate_data_covariables | 0.011 | 0.002 | 0.013 | |
| generate_dataset | 0.010 | 0.002 | 0.012 | |