Yannis Schumann
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:35 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.0.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-05-09 05:06:19 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 05:07:43 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 84.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 31.154 1.488 22.338
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-05-09 05:07:29.279063 INFO::Formatting Data.
2024-05-09 05:07:29.280807 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:29.297093 INFO::Removing potential empty rows and columns
2024-05-09 05:07:29.673121 INFO::Found 0 missing values.
2024-05-09 05:07:29.678621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:29.679655 INFO::Done
2024-05-09 05:07:29.680627 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:29.697925 INFO::Starting hierarchical adjustment
2024-05-09 05:07:29.699272 INFO::Found 3 batches.
2024-05-09 05:07:29.700234 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:29.70213 INFO::Using default BPPARAM
2024-05-09 05:07:29.703225 INFO::Processing subtree level 1
2024-05-09 05:07:29.83848 INFO::Adjusting the last 1 batches sequentially
2024-05-09 05:07:29.841275 INFO::Done
2024-05-09 05:07:29.842254 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:29.846254 INFO::ASW Batch was 0.0473882838880103 prior to batch effect correction and is now 0.0473882838880103 .
2024-05-09 05:07:29.848149 INFO::Total function execution time is 0.569758415222168 s and adjustment time is 0.142351388931274 s ( 24.98 )
2024-05-09 05:07:29.869169 INFO::Formatting Data.
2024-05-09 05:07:29.87027 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:29.871693 INFO::Removing potential empty rows and columns
2024-05-09 05:07:29.873502 INFO::Found 0 missing values.
2024-05-09 05:07:29.875009 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.
2024-05-09 05:07:29.891972 INFO::Formatting Data.
2024-05-09 05:07:29.893081 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:29.894518 INFO::Removing potential empty rows and columns
2024-05-09 05:07:29.896273 INFO::Found 0 missing values.
2024-05-09 05:07:29.897813 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.
2024-05-09 05:07:29.922099 INFO::Formatting Data.
2024-05-09 05:07:29.923161 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:29.924409 INFO::Removing potential empty rows and columns
2024-05-09 05:07:29.925921 INFO::Found 0 missing values.
2024-05-09 05:07:29.927276 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.
2024-05-09 05:07:29.93386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:29.93473 INFO::Done
2024-05-09 05:07:29.935528 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:29.938376 INFO::Starting hierarchical adjustment
2024-05-09 05:07:29.939471 INFO::Found 2 batches.
2024-05-09 05:07:29.940255 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:29.941155 INFO::Using default BPPARAM
2024-05-09 05:07:29.941952 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:29.943331 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:29.973492 INFO::Done
2024-05-09 05:07:29.974419 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:29.977232 INFO::ASW Batch was 0.0508471951306592 prior to batch effect correction and is now -0.115167132167889 .
2024-05-09 05:07:29.978459 INFO::Total function execution time is 0.0564024448394775 s and adjustment time is 0.0342247486114502 s ( 60.68 )
2024-05-09 05:07:29.982364 INFO::Formatting Data.
2024-05-09 05:07:29.983452 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:29.996064 INFO::Formatting Data.
2024-05-09 05:07:29.997185 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:29.998628 INFO::Removing potential empty rows and columns
2024-05-09 05:07:30.00028 INFO::Found 0 missing values.
2024-05-09 05:07:30.004848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:30.005833 INFO::Done
2024-05-09 05:07:30.006712 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:30.009814 INFO::Starting hierarchical adjustment
2024-05-09 05:07:30.010989 INFO::Found 2 batches.
2024-05-09 05:07:30.011895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:30.012821 INFO::Using default BPPARAM
2024-05-09 05:07:30.013642 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:30.015144 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:30.037242 INFO::Done
2024-05-09 05:07:30.038244 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:30.041369 INFO::ASW Batch was -0.0263135661857268 prior to batch effect correction and is now -0.119527295311237 .
2024-05-09 05:07:30.042691 INFO::Total function execution time is 0.046644926071167 s and adjustment time is 0.0265028476715088 s ( 56.82 )
2024-05-09 05:07:30.044503 INFO::Formatting Data.
2024-05-09 05:07:30.045548 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:30.046992 INFO::Removing potential empty rows and columns
2024-05-09 05:07:30.048688 INFO::Found 0 missing values.
2024-05-09 05:07:30.053476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:30.054482 INFO::Done
2024-05-09 05:07:30.055465 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:30.058648 INFO::Starting hierarchical adjustment
2024-05-09 05:07:30.059915 INFO::Found 2 batches.
2024-05-09 05:07:30.060847 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:30.061866 INFO::Using default BPPARAM
2024-05-09 05:07:30.06274 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:30.064268 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:30.086419 INFO::Done
2024-05-09 05:07:30.087409 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:30.090416 INFO::ASW Batch was -0.0263135661857268 prior to batch effect correction and is now -0.119527295311237 .
2024-05-09 05:07:30.091677 INFO::Total function execution time is 0.0471956729888916 s and adjustment time is 0.0267581939697266 s ( 56.7 )
2024-05-09 05:07:33.01735 INFO::Formatting Data.
2024-05-09 05:07:33.01836 INFO::Recognized SummarizedExperiment
2024-05-09 05:07:33.019073 INFO::Typecasting input to dataframe.
2024-05-09 05:07:33.06271 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:33.064251 INFO::Removing potential empty rows and columns
2024-05-09 05:07:33.069499 INFO::Found 0 missing values.
2024-05-09 05:07:33.079658 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:33.080508 INFO::Done
2024-05-09 05:07:33.08123 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:33.08629 INFO::Starting hierarchical adjustment
2024-05-09 05:07:33.087373 INFO::Found 2 batches.
2024-05-09 05:07:33.088086 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:33.089451 INFO::Using default BPPARAM
2024-05-09 05:07:33.090178 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:33.091519 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:33.198852 INFO::Done
2024-05-09 05:07:33.199885 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:33.204368 INFO::ASW Batch was -0.00233822516074262 prior to batch effect correction and is now -0.0926706494677978 .
2024-05-09 05:07:33.205488 INFO::Total function execution time is 0.188593864440918 s and adjustment time is 0.111713647842407 s ( 59.24 )
2024-05-09 05:07:33.228196 INFO::Formatting Data.
2024-05-09 05:07:33.229061 INFO::Recognized SummarizedExperiment
2024-05-09 05:07:33.229768 INFO::Typecasting input to dataframe.
2024-05-09 05:07:33.241502 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:33.243016 INFO::Removing potential empty rows and columns
2024-05-09 05:07:33.247948 INFO::Found 0 missing values.
2024-05-09 05:07:33.257609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:33.25846 INFO::Done
2024-05-09 05:07:33.259178 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:33.263828 INFO::Starting hierarchical adjustment
2024-05-09 05:07:33.264843 INFO::Found 2 batches.
2024-05-09 05:07:33.265533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:33.266321 INFO::Using default BPPARAM
2024-05-09 05:07:33.266984 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:33.268311 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:33.301509 INFO::Done
2024-05-09 05:07:33.302373 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:33.306916 INFO::ASW Batch was -0.00336370021420885 prior to batch effect correction and is now -0.00336370021420885 .
2024-05-09 05:07:33.308081 INFO::Total function execution time is 0.0798289775848389 s and adjustment time is 0.036851167678833 s ( 46.16 )
2024-05-09 05:07:33.330625 INFO::Formatting Data.
2024-05-09 05:07:33.331552 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:33.33265 INFO::Removing potential empty rows and columns
2024-05-09 05:07:33.333943 INFO::Found 0 missing values.
2024-05-09 05:07:33.337735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:33.338501 INFO::Done
2024-05-09 05:07:33.339196 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:33.341612 INFO::Starting hierarchical adjustment
2024-05-09 05:07:33.342556 INFO::Found 3 batches.
2024-05-09 05:07:33.343268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:33.344036 INFO::Using default BPPARAM
2024-05-09 05:07:33.344715 INFO::Processing subtree level 1
2024-05-09 05:07:33.555911 INFO::Adjusting the last 1 batches sequentially
2024-05-09 05:07:33.558368 INFO::Done
2024-05-09 05:07:33.559251 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:33.562732 INFO::ASW Batch was -0.0857802487041473 prior to batch effect correction and is now -0.175852458166886 .
2024-05-09 05:07:33.564276 INFO::Total function execution time is 0.233581066131592 s and adjustment time is 0.21599292755127 s ( 92.47 )
2024-05-09 05:07:33.587695 INFO::Skipping initial DF formatting
2024-05-09 05:07:33.588683 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:33.594818 INFO::Starting hierarchical adjustment
2024-05-09 05:07:33.596016 INFO::Found 5 batches.
2024-05-09 05:07:33.596824 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:33.597733 INFO::Using default BPPARAM
2024-05-09 05:07:33.598517 INFO::Processing subtree level 1
2024-05-09 05:07:33.786164 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:33.788357 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:33.821941 INFO::Done
2024-05-09 05:07:33.822844 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:33.829447 INFO::ASW Batch was 0.523029288211002 prior to batch effect correction and is now 0.523029288211002 .
2024-05-09 05:07:33.830475 INFO::ASW Label was 0.396211846896013 prior to batch effect correction and is now 0.396211846896013 .
2024-05-09 05:07:33.831803 INFO::Total function execution time is 0.244091033935547 s and adjustment time is 0.226139307022095 s ( 92.65 )
2024-05-09 05:07:33.85858 INFO::Formatting Data.
2024-05-09 05:07:33.859618 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:33.860882 INFO::Removing potential empty rows and columns
2024-05-09 05:07:33.86229 INFO::Found 0 missing values.
2024-05-09 05:07:33.868263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:33.869148 INFO::Done
2024-05-09 05:07:33.86993 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:33.874052 INFO::Starting hierarchical adjustment
2024-05-09 05:07:33.875168 INFO::Found 5 batches.
2024-05-09 05:07:33.875942 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:33.876801 INFO::Using default BPPARAM
2024-05-09 05:07:33.877572 INFO::Processing subtree level 1
2024-05-09 05:07:34.034741 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:34.037076 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:34.062346 INFO::Done
2024-05-09 05:07:34.063396 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:34.068339 INFO::ASW Batch was 0.231136066092128 prior to batch effect correction and is now -0.0734068399251454 .
2024-05-09 05:07:34.06937 INFO::ASW Label was 0.312767894620891 prior to batch effect correction and is now 0.854693810170406 .
2024-05-09 05:07:34.070687 INFO::Total function execution time is 0.212121725082397 s and adjustment time is 0.187366485595703 s ( 88.33 )
2024-05-09 05:07:34.072015 INFO::Formatting Data.
2024-05-09 05:07:34.073015 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:34.074446 INFO::Removing potential empty rows and columns
2024-05-09 05:07:34.076002 INFO::Found 0 missing values.
2024-05-09 05:07:34.082529 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:34.083518 INFO::Done
2024-05-09 05:07:34.084287 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:34.088723 INFO::Starting hierarchical adjustment
2024-05-09 05:07:34.089993 INFO::Found 5 batches.
2024-05-09 05:07:34.090785 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:34.091741 INFO::Using default BPPARAM
2024-05-09 05:07:34.092518 INFO::Processing subtree level 1
2024-05-09 05:07:34.244305 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:34.246398 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:34.268404 INFO::Done
2024-05-09 05:07:34.269356 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:34.273862 INFO::ASW Batch was 0.231136066092128 prior to batch effect correction and is now -0.0734068399251454 .
2024-05-09 05:07:34.274847 INFO::ASW Label was 0.312767894620891 prior to batch effect correction and is now 0.854693810170406 .
2024-05-09 05:07:34.276075 INFO::Total function execution time is 0.204062700271606 s and adjustment time is 0.178679943084717 s ( 87.56 )
2024-05-09 05:07:34.295773 INFO::Formatting Data.
2024-05-09 05:07:34.296867 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:34.298234 INFO::Removing potential empty rows and columns
2024-05-09 05:07:34.299741 INFO::Found 0 missing values.
2024-05-09 05:07:34.306047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:34.30695 INFO::Done
2024-05-09 05:07:34.307793 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:34.312028 INFO::Starting hierarchical adjustment
2024-05-09 05:07:34.313191 INFO::Found 5 batches.
2024-05-09 05:07:34.31402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:34.314924 INFO::Using default BPPARAM
2024-05-09 05:07:34.315758 INFO::Processing subtree level 1
2024-05-09 05:07:34.470797 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:34.473017 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:34.496276 INFO::Done
2024-05-09 05:07:34.497293 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:34.502011 INFO::ASW Batch was 0.408802998940882 prior to batch effect correction and is now -0.0646822976561165 .
2024-05-09 05:07:34.503008 INFO::ASW Label was 0.413870332338015 prior to batch effect correction and is now 0.860565249984586 .
2024-05-09 05:07:34.504301 INFO::Total function execution time is 0.208555936813354 s and adjustment time is 0.183309078216553 s ( 87.89 )
2024-05-09 05:07:34.505578 INFO::Formatting Data.
2024-05-09 05:07:34.5065 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:34.507845 INFO::Removing potential empty rows and columns
2024-05-09 05:07:34.509307 INFO::Found 0 missing values.
2024-05-09 05:07:34.515863 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:34.516789 INFO::Done
2024-05-09 05:07:34.517575 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:34.521835 INFO::Starting hierarchical adjustment
2024-05-09 05:07:34.522964 INFO::Found 5 batches.
2024-05-09 05:07:34.523782 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:34.524648 INFO::Using default BPPARAM
2024-05-09 05:07:34.525424 INFO::Processing subtree level 1
2024-05-09 05:07:34.675542 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:34.677704 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:34.700317 INFO::Done
2024-05-09 05:07:34.701256 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:34.705813 INFO::ASW Batch was 0.408802998940882 prior to batch effect correction and is now -0.0646822976561165 .
2024-05-09 05:07:34.706797 INFO::ASW Label was 0.413870332338015 prior to batch effect correction and is now 0.860565249984586 .
2024-05-09 05:07:34.708004 INFO::Total function execution time is 0.202411413192749 s and adjustment time is 0.177555799484253 s ( 87.72 )
2024-05-09 05:07:34.7275 INFO::Formatting Data.
2024-05-09 05:07:34.728544 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:34.729819 INFO::Removing potential empty rows and columns
2024-05-09 05:07:34.731273 INFO::Found 0 missing values.
2024-05-09 05:07:34.735275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:34.736109 INFO::Done
2024-05-09 05:07:34.736849 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:34.740928 INFO::Starting hierarchical adjustment
2024-05-09 05:07:34.742021 INFO::Found 2 batches.
2024-05-09 05:07:34.742799 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:34.743757 INFO::Using default BPPARAM
2024-05-09 05:07:34.74451 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:34.745849 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:34.766562 INFO::Done
2024-05-09 05:07:34.767499 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:34.771607 INFO::ASW Batch was 0.669870052689126 prior to batch effect correction and is now -0.0149743357264609 .
2024-05-09 05:07:34.772497 INFO::ASW Label was 0.351770097846087 prior to batch effect correction and is now 0.864886293006383 .
2024-05-09 05:07:34.773636 INFO::Total function execution time is 0.0462074279785156 s and adjustment time is 0.0247623920440674 s ( 53.59 )
2024-05-09 05:07:34.774771 INFO::Formatting Data.
2024-05-09 05:07:34.775669 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:34.776897 INFO::Removing potential empty rows and columns
2024-05-09 05:07:34.778317 INFO::Found 0 missing values.
2024-05-09 05:07:34.782341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:34.783212 INFO::Done
2024-05-09 05:07:34.783974 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:34.788063 INFO::Starting hierarchical adjustment
2024-05-09 05:07:34.789207 INFO::Found 2 batches.
2024-05-09 05:07:34.790046 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:34.790898 INFO::Using default BPPARAM
2024-05-09 05:07:34.791707 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:34.793011 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:34.814452 INFO::Done
2024-05-09 05:07:34.815358 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:34.819437 INFO::ASW Batch was 0.669870052689126 prior to batch effect correction and is now -0.0149743357264609 .
2024-05-09 05:07:34.820326 INFO::ASW Label was 0.351770097846087 prior to batch effect correction and is now 0.864886293006383 .
2024-05-09 05:07:34.821394 INFO::Total function execution time is 0.0466358661651611 s and adjustment time is 0.0255093574523926 s ( 54.7 )
2024-05-09 05:07:34.837412 INFO::Formatting Data.
2024-05-09 05:07:34.838408 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:34.839611 INFO::Removing potential empty rows and columns
2024-05-09 05:07:34.840839 INFO::Found 0 missing values.
2024-05-09 05:07:34.843884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:34.84466 INFO::Done
2024-05-09 05:07:34.845385 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:34.848052 INFO::Starting hierarchical adjustment
2024-05-09 05:07:34.849056 INFO::Found 2 batches.
2024-05-09 05:07:34.849827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:34.850678 INFO::Using default BPPARAM
2024-05-09 05:07:34.851474 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:34.852821 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:34.898935 INFO::Done
2024-05-09 05:07:34.899842 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:34.902573 INFO::ASW Batch was -0.12717673443205 prior to batch effect correction and is now -0.139363212058071 .
2024-05-09 05:07:34.903757 INFO::Total function execution time is 0.0664162635803223 s and adjustment time is 0.0500686168670654 s ( 75.39 )
2024-05-09 05:07:34.920936 INFO::Formatting Data.
2024-05-09 05:07:34.921982 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:34.923225 INFO::Removing potential empty rows and columns
2024-05-09 05:07:34.924675 INFO::Found 0 missing values.
2024-05-09 05:07:34.926291 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.
2024-05-09 05:07:34.954537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:34.955603 INFO::Done
2024-05-09 05:07:34.95638 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:34.960534 INFO::Starting hierarchical adjustment
2024-05-09 05:07:34.961653 INFO::Found 2 batches.
2024-05-09 05:07:34.962411 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:34.963288 INFO::Using default BPPARAM
2024-05-09 05:07:34.964034 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:34.965446 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:34.996342 INFO::Done
2024-05-09 05:07:34.99742 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:35.001942 INFO::ASW Batch was 0.738450411174094 prior to batch effect correction and is now -7.36067826265507e-05 .
2024-05-09 05:07:35.002891 INFO::ASW Label was 0.278885177254266 prior to batch effect correction and is now 0.869234863961421 .
2024-05-09 05:07:35.004006 INFO::Total function execution time is 0.0831267833709717 s and adjustment time is 0.034700870513916 s ( 41.74 )
2024-05-09 05:07:35.005121 INFO::Formatting Data.
2024-05-09 05:07:35.005975 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:35.007326 INFO::Removing potential empty rows and columns
2024-05-09 05:07:35.008772 INFO::Found 0 missing values.
2024-05-09 05:07:35.010046 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.
2024-05-09 05:07:35.01722 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:35.018115 INFO::Done
2024-05-09 05:07:35.018869 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:35.023198 INFO::Starting hierarchical adjustment
2024-05-09 05:07:35.024271 INFO::Found 2 batches.
2024-05-09 05:07:35.025036 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:35.02603 INFO::Using default BPPARAM
2024-05-09 05:07:35.026798 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:35.028264 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:35.054207 INFO::Done
2024-05-09 05:07:35.055106 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:35.059366 INFO::ASW Batch was 0.738450411174094 prior to batch effect correction and is now -7.36067826265507e-05 .
2024-05-09 05:07:35.060261 INFO::ASW Label was 0.278885177254266 prior to batch effect correction and is now 0.869234863961421 .
2024-05-09 05:07:35.061421 INFO::Total function execution time is 0.0563032627105713 s and adjustment time is 0.0301342010498047 s ( 53.52 )
2024-05-09 05:07:35.394824 INFO::Formatting Data.
2024-05-09 05:07:35.395994 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:35.397334 INFO::Removing potential empty rows and columns
2024-05-09 05:07:35.398887 INFO::Found 0 missing values.
2024-05-09 05:07:35.403652 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:35.40456 INFO::Done
2024-05-09 05:07:35.405379 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:35.408886 INFO::Starting hierarchical adjustment
2024-05-09 05:07:35.410105 INFO::Found 3 batches.
2024-05-09 05:07:35.410918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:35.411891 INFO::Using default BPPARAM
2024-05-09 05:07:35.412667 INFO::Processing subtree level 1
2024-05-09 05:07:35.541904 INFO::Adjusting the last 1 batches sequentially
2024-05-09 05:07:35.54427 INFO::Done
2024-05-09 05:07:35.545162 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:35.548609 INFO::ASW Batch was -0.0830180301160073 prior to batch effect correction and is now -0.0830180301160073 .
2024-05-09 05:07:35.550077 INFO::Total function execution time is 0.155296564102173 s and adjustment time is 0.1344153881073 s ( 86.55 )
2024-05-09 05:07:35.551665 INFO::Formatting Data.
2024-05-09 05:07:35.552612 INFO::Typecasting input to dataframe.
2024-05-09 05:07:35.553725 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:35.555073 INFO::Removing potential empty rows and columns
2024-05-09 05:07:35.556707 INFO::Found 0 missing values.
2024-05-09 05:07:35.561358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:35.562278 INFO::Done
2024-05-09 05:07:35.563117 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:35.566076 INFO::Starting hierarchical adjustment
2024-05-09 05:07:35.567233 INFO::Found 3 batches.
2024-05-09 05:07:35.568047 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:35.568952 INFO::Using default BPPARAM
2024-05-09 05:07:35.569808 INFO::Processing subtree level 1
2024-05-09 05:07:35.688119 INFO::Adjusting the last 1 batches sequentially
2024-05-09 05:07:35.690362 INFO::Done
2024-05-09 05:07:35.691255 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:35.694599 INFO::ASW Batch was -0.0830180301160073 prior to batch effect correction and is now -0.0830180301160073 .
2024-05-09 05:07:35.695963 INFO::Total function execution time is 0.144270181655884 s and adjustment time is 0.123386859893799 s ( 85.52 )
2024-05-09 05:07:35.71422 INFO::Formatting Data.
2024-05-09 05:07:35.715248 INFO::Typecasting input to dataframe.
2024-05-09 05:07:35.716447 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:35.717643 INFO::Removing potential empty rows and columns
2024-05-09 05:07:35.719179 INFO::Found 0 missing values.
2024-05-09 05:07:35.723762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:35.724638 INFO::Done
2024-05-09 05:07:35.725393 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:35.7282 INFO::Starting hierarchical adjustment
2024-05-09 05:07:35.729249 INFO::Found 3 batches.
2024-05-09 05:07:35.730045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:35.73094 INFO::Using default BPPARAM
2024-05-09 05:07:35.731748 INFO::Processing subtree level 1
2024-05-09 05:07:35.848387 INFO::Adjusting the last 1 batches sequentially
2024-05-09 05:07:35.850726 INFO::Done
2024-05-09 05:07:35.851644 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:35.855087 INFO::ASW Batch was -0.140778926381603 prior to batch effect correction and is now -0.140778926381603 .
2024-05-09 05:07:35.856472 INFO::Total function execution time is 0.142274141311646 s and adjustment time is 0.121685266494751 s ( 85.53 )
2024-05-09 05:07:36.048014 INFO::Formatting Data.
2024-05-09 05:07:36.049144 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:36.050843 INFO::Removing potential empty rows and columns
2024-05-09 05:07:36.055441 INFO::Found 1000 missing values.
2024-05-09 05:07:36.085848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:36.08677 INFO::Done
2024-05-09 05:07:36.087572 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:36.095305 INFO::Starting hierarchical adjustment
2024-05-09 05:07:36.096424 INFO::Found 10 batches.
2024-05-09 05:07:36.097187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:36.098063 INFO::Using default BPPARAM
2024-05-09 05:07:36.098818 INFO::Processing subtree level 1
2024-05-09 05:07:36.28105 INFO::Processing subtree level 2
2024-05-09 05:07:36.551392 INFO::Adjusting the last 1 batches sequentially
2024-05-09 05:07:36.553943 INFO::Done
2024-05-09 05:07:36.554827 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:36.562636 INFO::ASW Batch was 0.475096986557959 prior to batch effect correction and is now 0.475096986557959 .
2024-05-09 05:07:36.563628 INFO::ASW Label was 0.363945640084739 prior to batch effect correction and is now 0.363945640084739 .
2024-05-09 05:07:36.564887 INFO::Total function execution time is 0.516925811767578 s and adjustment time is 0.457752466201782 s ( 88.55 )
2024-05-09 05:07:36.566125 INFO::Formatting Data.
2024-05-09 05:07:36.567016 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:36.568723 INFO::Removing potential empty rows and columns
2024-05-09 05:07:36.573508 INFO::Found 1000 missing values.
2024-05-09 05:07:36.60563 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:36.606648 INFO::Done
2024-05-09 05:07:36.607511 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:36.615411 INFO::Starting hierarchical adjustment
2024-05-09 05:07:36.616637 INFO::Found 10 batches.
2024-05-09 05:07:37.905283 INFO::Set up parallel execution backend with 2 workers
2024-05-09 05:07:37.906332 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-09 05:07:39.232635 INFO::Adjusting the last 2 batches sequentially
2024-05-09 05:07:39.234387 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-09 05:07:39.258829 INFO::Done
2024-05-09 05:07:39.259647 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:39.266059 INFO::ASW Batch was 0.475096986557959 prior to batch effect correction and is now 0.475096986557959 .
2024-05-09 05:07:39.26684 INFO::ASW Label was 0.363945640084739 prior to batch effect correction and is now 0.363945640084739 .
2024-05-09 05:07:39.267836 INFO::Total function execution time is 2.70179128646851 s and adjustment time is 2.64245223999023 s ( 97.8 )
2024-05-09 05:07:39.454762 INFO::Formatting Data.
2024-05-09 05:07:39.455989 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:39.457389 INFO::Removing potential empty rows and columns
2024-05-09 05:07:39.45914 INFO::Found 0 missing values.
2024-05-09 05:07:39.465228 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:39.466141 INFO::Done
2024-05-09 05:07:39.466902 INFO::Acquiring quality metrics before batch effect correction.
2024-05-09 05:07:39.47103 INFO::Starting hierarchical adjustment
2024-05-09 05:07:39.472197 INFO::Found 3 batches.
2024-05-09 05:07:39.472968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-09 05:07:39.473896 INFO::Using default BPPARAM
2024-05-09 05:07:39.474653 INFO::Processing subtree level 1
2024-05-09 05:07:39.607467 INFO::Adjusting the last 1 batches sequentially
2024-05-09 05:07:39.609788 INFO::Done
2024-05-09 05:07:39.610664 INFO::Acquiring quality metrics after batch effect correction.
2024-05-09 05:07:39.615163 INFO::ASW Batch was 0.161467154880045 prior to batch effect correction and is now -0.119297245492757 .
2024-05-09 05:07:39.616099 INFO::ASW Label was -0.203219490586798 prior to batch effect correction and is now 0.0184848538283768 .
2024-05-09 05:07:39.617369 INFO::Total function execution time is 0.162689447402954 s and adjustment time is 0.137805938720703 s ( 84.7 )
2024-05-09 05:07:39.789618 INFO::Formatting Data.
2024-05-09 05:07:39.790621 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:39.791813 INFO::Removing potential empty rows and columns
2024-05-09 05:07:39.793251 INFO::Found 2 missing values.
2024-05-09 05:07:39.797345 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:39.798124 INFO::Done
2024-05-09 05:07:39.83633 INFO::Found NA in Reference column
2024-05-09 05:07:39.85013 INFO::Require at least two references per batch.
2024-05-09 05:07:39.879668 INFO::Formatting Data.
2024-05-09 05:07:39.88061 INFO::Recognized SummarizedExperiment
2024-05-09 05:07:39.881319 INFO::Typecasting input to dataframe.
2024-05-09 05:07:39.895553 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:39.897205 INFO::Removing potential empty rows and columns
2024-05-09 05:07:39.902993 INFO::Found 0 missing values.
2024-05-09 05:07:39.914469 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:39.915466 INFO::Done
2024-05-09 05:07:39.943579 INFO::Formatting Data.
2024-05-09 05:07:39.944614 INFO::Recognized SummarizedExperiment
2024-05-09 05:07:39.945372 INFO::Typecasting input to dataframe.
2024-05-09 05:07:39.971339 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:39.973005 INFO::Removing potential empty rows and columns
2024-05-09 05:07:39.978958 INFO::Found 0 missing values.
2024-05-09 05:07:39.998694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:39.999738 INFO::Done
2024-05-09 05:07:40.02418 INFO::Formatting Data.
2024-05-09 05:07:40.025216 INFO::Recognized SummarizedExperiment
2024-05-09 05:07:40.026038 INFO::Typecasting input to dataframe.
2024-05-09 05:07:40.053029 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:40.054458 INFO::Removing potential empty rows and columns
2024-05-09 05:07:40.056034 INFO::Found 0 missing values.
2024-05-09 05:07:40.0575 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.
2024-05-09 05:07:40.064664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:40.065587 INFO::Done
2024-05-09 05:07:40.081234 INFO::Formatting Data.
2024-05-09 05:07:40.082278 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:40.083454 INFO::Removing potential empty rows and columns
2024-05-09 05:07:40.084884 INFO::Found 0 missing values.
2024-05-09 05:07:40.089565 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:40.09039 INFO::Done
2024-05-09 05:07:40.106762 INFO::Formatting Data.
2024-05-09 05:07:40.107754 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:40.108901 INFO::Removing potential empty rows and columns
2024-05-09 05:07:40.110295 INFO::Found 0 missing values.
2024-05-09 05:07:40.114531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:40.115329 INFO::Done
2024-05-09 05:07:40.156801 INFO::Formatting Data.
2024-05-09 05:07:40.157824 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:40.159237 INFO::Removing potential empty rows and columns
2024-05-09 05:07:40.160838 INFO::Found 1 missing values.
2024-05-09 05:07:40.164703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:40.165521 INFO::Done
2024-05-09 05:07:40.192816 INFO::Formatting Data.
2024-05-09 05:07:40.193851 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:40.195029 INFO::Removing potential empty rows and columns
2024-05-09 05:07:40.196416 INFO::Found 2 missing values.
2024-05-09 05:07:40.197697 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.
2024-05-09 05:07:40.201009 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:40.201785 INFO::Done
2024-05-09 05:07:40.216583 INFO::Formatting Data.
2024-05-09 05:07:40.217586 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:40.218793 INFO::Removing potential empty rows and columns
2024-05-09 05:07:40.220136 INFO::Found 2 missing values.
2024-05-09 05:07:40.222416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:40.223181 INFO::Done
2024-05-09 05:07:40.238815 INFO::Formatting Data.
2024-05-09 05:07:40.239943 INFO::Typecasting input to dataframe.
2024-05-09 05:07:40.241039 INFO::Replacing NaNs with NAs.
2024-05-09 05:07:40.242249 INFO::Removing potential empty rows and columns
2024-05-09 05:07:40.243709 INFO::Found 0 missing values.
2024-05-09 05:07:40.248165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-09 05:07:40.24902 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.484 4.363 25.246
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.154 | 1.488 | 22.338 | |
| compute_asw | 0.036 | 0.000 | 0.036 | |
| count_existing | 0.016 | 0.004 | 0.020 | |
| generate_data_covariables | 0.017 | 0.000 | 0.017 | |
| generate_dataset | 0.016 | 0.000 | 0.020 | |