Yannis Schumann
| Snapshot Date: 2024-07-07 14:00 -0400 (Sun, 07 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-08 11:44 -0400 (Mon, 08 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
| 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 154/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | NA | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.1.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.1.0.tar.gz |
| StartedAt: 2024-07-06 03:09:56 -0000 (Sat, 06 Jul 2024) |
| EndedAt: 2024-07-06 03:11:15 -0000 (Sat, 06 Jul 2024) |
| EllapsedTime: 79.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
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 ‘1.1.0’
* 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 31.556 1.31 22.427
* 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/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: 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")
2024-07-06 03:11:00.439023 INFO::Formatting Data.
2024-07-06 03:11:00.441075 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:00.45928 INFO::Removing potential empty rows and columns
2024-07-06 03:11:00.909389 INFO::Found 0 missing values.
2024-07-06 03:11:00.913956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:00.914847 INFO::Done
2024-07-06 03:11:00.915639 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:00.93123 INFO::Starting hierarchical adjustment
2024-07-06 03:11:00.932365 INFO::Found 3 batches.
2024-07-06 03:11:00.933124 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:00.934625 INFO::Using default BPPARAM
2024-07-06 03:11:00.935395 INFO::Processing subtree level 1
2024-07-06 03:11:01.060967 INFO::Adjusting the last 1 batches sequentially
2024-07-06 03:11:01.063373 INFO::Done
2024-07-06 03:11:01.064284 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:01.067867 INFO::ASW Batch was -0.116309422429384 prior to batch effect correction and is now -0.116309422429384 .
2024-07-06 03:11:01.069459 INFO::Total function execution time is 0.631522178649902 s and adjustment time is 0.131228446960449 s ( 20.78 )
2024-07-06 03:11:01.089738 INFO::Formatting Data.
2024-07-06 03:11:01.09075 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:01.092226 INFO::Removing potential empty rows and columns
2024-07-06 03:11:01.093863 INFO::Found 0 missing values.
2024-07-06 03:11:01.095295 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.
2024-07-06 03:11:01.111984 INFO::Formatting Data.
2024-07-06 03:11:01.11308 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:01.114459 INFO::Removing potential empty rows and columns
2024-07-06 03:11:01.11608 INFO::Found 0 missing values.
2024-07-06 03:11:01.117544 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.
2024-07-06 03:11:01.140714 INFO::Formatting Data.
2024-07-06 03:11:01.141686 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:01.14291 INFO::Removing potential empty rows and columns
2024-07-06 03:11:01.144361 INFO::Found 0 missing values.
2024-07-06 03:11:01.14561 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.
2024-07-06 03:11:01.152065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:01.152941 INFO::Done
2024-07-06 03:11:01.15366 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:01.156484 INFO::Starting hierarchical adjustment
2024-07-06 03:11:01.157568 INFO::Found 2 batches.
2024-07-06 03:11:01.158346 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:01.159249 INFO::Using default BPPARAM
2024-07-06 03:11:01.15999 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:01.161319 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:01.196388 INFO::Done
2024-07-06 03:11:01.197438 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:01.200532 INFO::ASW Batch was -0.0537233666264514 prior to batch effect correction and is now -0.104693718545048 .
2024-07-06 03:11:01.201746 INFO::Total function execution time is 0.0610663890838623 s and adjustment time is 0.0389847755432129 s ( 63.84 )
2024-07-06 03:11:01.206092 INFO::Formatting Data.
2024-07-06 03:11:01.207067 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:01.21931 INFO::Formatting Data.
2024-07-06 03:11:01.220258 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:01.221437 INFO::Removing potential empty rows and columns
2024-07-06 03:11:01.222842 INFO::Found 0 missing values.
2024-07-06 03:11:01.226918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:01.22779 INFO::Done
2024-07-06 03:11:01.228491 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:01.231235 INFO::Starting hierarchical adjustment
2024-07-06 03:11:01.232266 INFO::Found 2 batches.
2024-07-06 03:11:01.232996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:01.233859 INFO::Using default BPPARAM
2024-07-06 03:11:01.23462 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:01.235951 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:01.256887 INFO::Done
2024-07-06 03:11:01.257818 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:01.260782 INFO::ASW Batch was -0.0974982007704577 prior to batch effect correction and is now -0.13629383529028 .
2024-07-06 03:11:01.262014 INFO::Total function execution time is 0.0427193641662598 s and adjustment time is 0.0248024463653564 s ( 58.06 )
2024-07-06 03:11:01.263623 INFO::Formatting Data.
2024-07-06 03:11:01.264564 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:01.265803 INFO::Removing potential empty rows and columns
2024-07-06 03:11:01.267349 INFO::Found 0 missing values.
2024-07-06 03:11:01.273835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:01.274741 INFO::Done
2024-07-06 03:11:01.27552 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:01.278336 INFO::Starting hierarchical adjustment
2024-07-06 03:11:01.279447 INFO::Found 2 batches.
2024-07-06 03:11:01.280212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:01.281048 INFO::Using default BPPARAM
2024-07-06 03:11:01.281778 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:01.283128 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:01.304085 INFO::Done
2024-07-06 03:11:01.304962 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:01.307766 INFO::ASW Batch was -0.0974982007704577 prior to batch effect correction and is now -0.13629383529028 .
2024-07-06 03:11:01.308956 INFO::Total function execution time is 0.0453212261199951 s and adjustment time is 0.024843692779541 s ( 54.82 )
2024-07-06 03:11:04.217544 INFO::Formatting Data.
2024-07-06 03:11:04.218532 INFO::Recognized SummarizedExperiment
2024-07-06 03:11:04.219242 INFO::Typecasting input to dataframe.
2024-07-06 03:11:04.303833 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:04.305388 INFO::Removing potential empty rows and columns
2024-07-06 03:11:04.310588 INFO::Found 0 missing values.
2024-07-06 03:11:04.320566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:04.321369 INFO::Done
2024-07-06 03:11:04.322047 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:04.326833 INFO::Starting hierarchical adjustment
2024-07-06 03:11:04.327746 INFO::Found 2 batches.
2024-07-06 03:11:04.328406 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:04.329756 INFO::Using default BPPARAM
2024-07-06 03:11:04.330448 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:04.331685 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:04.407659 INFO::Done
2024-07-06 03:11:04.408452 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:04.413145 INFO::ASW Batch was -0.0053196560031268 prior to batch effect correction and is now -0.0990456949249812 .
2024-07-06 03:11:04.414213 INFO::Total function execution time is 0.197149276733398 s and adjustment time is 0.0800881385803223 s ( 40.62 )
2024-07-06 03:11:04.435717 INFO::Formatting Data.
2024-07-06 03:11:04.436539 INFO::Recognized SummarizedExperiment
2024-07-06 03:11:04.437153 INFO::Typecasting input to dataframe.
2024-07-06 03:11:04.448163 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:04.449527 INFO::Removing potential empty rows and columns
2024-07-06 03:11:04.454208 INFO::Found 0 missing values.
2024-07-06 03:11:04.46332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:04.464106 INFO::Done
2024-07-06 03:11:04.464751 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:04.469239 INFO::Starting hierarchical adjustment
2024-07-06 03:11:04.470181 INFO::Found 2 batches.
2024-07-06 03:11:04.470818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:04.471609 INFO::Using default BPPARAM
2024-07-06 03:11:04.472248 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:04.473441 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:04.505503 INFO::Done
2024-07-06 03:11:04.506291 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:04.510588 INFO::ASW Batch was 0.0147795252258912 prior to batch effect correction and is now 0.0147795252258912 .
2024-07-06 03:11:04.511577 INFO::Total function execution time is 0.0758359432220459 s and adjustment time is 0.0355112552642822 s ( 46.83 )
2024-07-06 03:11:04.532367 INFO::Formatting Data.
2024-07-06 03:11:04.533188 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:04.534203 INFO::Removing potential empty rows and columns
2024-07-06 03:11:04.535422 INFO::Found 0 missing values.
2024-07-06 03:11:04.539036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:04.539673 INFO::Done
2024-07-06 03:11:04.540297 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:04.542784 INFO::Starting hierarchical adjustment
2024-07-06 03:11:04.54371 INFO::Found 3 batches.
2024-07-06 03:11:04.544363 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:04.545192 INFO::Using default BPPARAM
2024-07-06 03:11:04.545861 INFO::Processing subtree level 1
2024-07-06 03:11:04.736863 INFO::Adjusting the last 1 batches sequentially
2024-07-06 03:11:04.739301 INFO::Done
2024-07-06 03:11:04.740187 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:04.743662 INFO::ASW Batch was -0.111418449910753 prior to batch effect correction and is now -0.183577276600529 .
2024-07-06 03:11:04.745097 INFO::Total function execution time is 0.212673664093018 s and adjustment time is 0.195744276046753 s ( 92.04 )
2024-07-06 03:11:04.767194 INFO::Skipping initial DF formatting
2024-07-06 03:11:04.768132 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:04.77401 INFO::Starting hierarchical adjustment
2024-07-06 03:11:04.775167 INFO::Found 5 batches.
2024-07-06 03:11:04.775952 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:04.776914 INFO::Using default BPPARAM
2024-07-06 03:11:04.777669 INFO::Processing subtree level 1
2024-07-06 03:11:04.954077 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:04.956278 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:04.98811 INFO::Done
2024-07-06 03:11:04.989014 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:04.994914 INFO::ASW Batch was 0.522659037055346 prior to batch effect correction and is now 0.522659037055346 .
2024-07-06 03:11:04.995742 INFO::ASW Label was 0.365400518630678 prior to batch effect correction and is now 0.365400518630678 .
2024-07-06 03:11:04.996895 INFO::Total function execution time is 0.229785442352295 s and adjustment time is 0.213173627853394 s ( 92.77 )
2024-07-06 03:11:05.022321 INFO::Formatting Data.
2024-07-06 03:11:05.023356 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:05.024606 INFO::Removing potential empty rows and columns
2024-07-06 03:11:05.026003 INFO::Found 0 missing values.
2024-07-06 03:11:05.032107 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:05.032969 INFO::Done
2024-07-06 03:11:05.033696 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:05.037652 INFO::Starting hierarchical adjustment
2024-07-06 03:11:05.038749 INFO::Found 5 batches.
2024-07-06 03:11:05.039505 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:05.040394 INFO::Using default BPPARAM
2024-07-06 03:11:05.041143 INFO::Processing subtree level 1
2024-07-06 03:11:05.187748 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:05.190367 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:05.216228 INFO::Done
2024-07-06 03:11:05.217148 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:05.221635 INFO::ASW Batch was 0.319548715632134 prior to batch effect correction and is now -0.0496263389218193 .
2024-07-06 03:11:05.2225 INFO::ASW Label was 0.432061984237013 prior to batch effect correction and is now 0.808464625710366 .
2024-07-06 03:11:05.223665 INFO::Total function execution time is 0.201395988464355 s and adjustment time is 0.177694082260132 s ( 88.23 )
2024-07-06 03:11:05.224879 INFO::Formatting Data.
2024-07-06 03:11:05.22574 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:05.227062 INFO::Removing potential empty rows and columns
2024-07-06 03:11:05.228489 INFO::Found 0 missing values.
2024-07-06 03:11:05.234677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:05.235592 INFO::Done
2024-07-06 03:11:05.236364 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:05.240685 INFO::Starting hierarchical adjustment
2024-07-06 03:11:05.241812 INFO::Found 5 batches.
2024-07-06 03:11:05.242568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:05.243571 INFO::Using default BPPARAM
2024-07-06 03:11:05.244384 INFO::Processing subtree level 1
2024-07-06 03:11:05.394861 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:05.39708 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:05.425159 INFO::Done
2024-07-06 03:11:05.426247 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:05.430979 INFO::ASW Batch was 0.319548715632134 prior to batch effect correction and is now -0.0496263389218193 .
2024-07-06 03:11:05.431895 INFO::ASW Label was 0.432061984237013 prior to batch effect correction and is now 0.808464625710366 .
2024-07-06 03:11:05.43311 INFO::Total function execution time is 0.208203792572021 s and adjustment time is 0.183528184890747 s ( 88.15 )
2024-07-06 03:11:05.453761 INFO::Formatting Data.
2024-07-06 03:11:05.454852 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:05.456275 INFO::Removing potential empty rows and columns
2024-07-06 03:11:05.457814 INFO::Found 0 missing values.
2024-07-06 03:11:05.464482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:05.465738 INFO::Done
2024-07-06 03:11:05.466581 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:05.471034 INFO::Starting hierarchical adjustment
2024-07-06 03:11:05.472213 INFO::Found 5 batches.
2024-07-06 03:11:05.472995 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:05.473942 INFO::Using default BPPARAM
2024-07-06 03:11:05.474718 INFO::Processing subtree level 1
2024-07-06 03:11:05.64531 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:05.64757 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:05.671596 INFO::Done
2024-07-06 03:11:05.672628 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:05.677744 INFO::ASW Batch was 0.366829872110726 prior to batch effect correction and is now -0.0807155403011565 .
2024-07-06 03:11:05.678817 INFO::ASW Label was 0.325731014522825 prior to batch effect correction and is now 0.90501993620087 .
2024-07-06 03:11:05.680371 INFO::Total function execution time is 0.226631164550781 s and adjustment time is 0.199593067169189 s ( 88.07 )
2024-07-06 03:11:05.681663 INFO::Formatting Data.
2024-07-06 03:11:05.682647 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:05.684009 INFO::Removing potential empty rows and columns
2024-07-06 03:11:05.685506 INFO::Found 0 missing values.
2024-07-06 03:11:05.691877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:05.692869 INFO::Done
2024-07-06 03:11:05.69368 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:05.698171 INFO::Starting hierarchical adjustment
2024-07-06 03:11:05.69943 INFO::Found 5 batches.
2024-07-06 03:11:05.700239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:05.701165 INFO::Using default BPPARAM
2024-07-06 03:11:05.701953 INFO::Processing subtree level 1
2024-07-06 03:11:05.863886 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:05.865997 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:05.889171 INFO::Done
2024-07-06 03:11:05.890109 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:05.894525 INFO::ASW Batch was 0.366829872110726 prior to batch effect correction and is now -0.0807155403011565 .
2024-07-06 03:11:05.895455 INFO::ASW Label was 0.325731014522825 prior to batch effect correction and is now 0.90501993620087 .
2024-07-06 03:11:05.896665 INFO::Total function execution time is 0.214985847473145 s and adjustment time is 0.189996957778931 s ( 88.38 )
2024-07-06 03:11:05.915594 INFO::Formatting Data.
2024-07-06 03:11:05.916631 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:05.917944 INFO::Removing potential empty rows and columns
2024-07-06 03:11:05.919449 INFO::Found 0 missing values.
2024-07-06 03:11:05.923532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:05.924392 INFO::Done
2024-07-06 03:11:05.925132 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:05.929256 INFO::Starting hierarchical adjustment
2024-07-06 03:11:05.930367 INFO::Found 2 batches.
2024-07-06 03:11:05.931181 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:05.932071 INFO::Using default BPPARAM
2024-07-06 03:11:05.932857 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:05.934419 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:05.960449 INFO::Done
2024-07-06 03:11:05.961506 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:05.966073 INFO::ASW Batch was 0.241256800825428 prior to batch effect correction and is now 0.0163145681003289 .
2024-07-06 03:11:05.967034 INFO::ASW Label was 0.804357117158257 prior to batch effect correction and is now 0.939815142601903 .
2024-07-06 03:11:05.968214 INFO::Total function execution time is 0.0526771545410156 s and adjustment time is 0.0300846099853516 s ( 57.11 )
2024-07-06 03:11:05.969412 INFO::Formatting Data.
2024-07-06 03:11:05.970294 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:05.971598 INFO::Removing potential empty rows and columns
2024-07-06 03:11:05.973102 INFO::Found 0 missing values.
2024-07-06 03:11:05.977374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:05.978276 INFO::Done
2024-07-06 03:11:05.979135 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:05.983599 INFO::Starting hierarchical adjustment
2024-07-06 03:11:05.984759 INFO::Found 2 batches.
2024-07-06 03:11:05.985534 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:05.986469 INFO::Using default BPPARAM
2024-07-06 03:11:05.987275 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:05.988684 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:06.011523 INFO::Done
2024-07-06 03:11:06.012491 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:06.053297 INFO::ASW Batch was 0.241256800825428 prior to batch effect correction and is now 0.0163145681003289 .
2024-07-06 03:11:06.054322 INFO::ASW Label was 0.804357117158257 prior to batch effect correction and is now 0.939815142601903 .
2024-07-06 03:11:06.055542 INFO::Total function execution time is 0.0861330032348633 s and adjustment time is 0.0269746780395508 s ( 31.32 )
2024-07-06 03:11:06.074549 INFO::Formatting Data.
2024-07-06 03:11:06.075714 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:06.077279 INFO::Removing potential empty rows and columns
2024-07-06 03:11:06.078972 INFO::Found 0 missing values.
2024-07-06 03:11:06.082709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:06.083723 INFO::Done
2024-07-06 03:11:06.084591 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:06.088024 INFO::Starting hierarchical adjustment
2024-07-06 03:11:06.089257 INFO::Found 2 batches.
2024-07-06 03:11:06.090194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:06.091278 INFO::Using default BPPARAM
2024-07-06 03:11:06.092113 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:06.093625 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:06.146629 INFO::Done
2024-07-06 03:11:06.147617 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:06.150703 INFO::ASW Batch was 0.168073098869162 prior to batch effect correction and is now -0.108821554305499 .
2024-07-06 03:11:06.152012 INFO::Total function execution time is 0.0775446891784668 s and adjustment time is 0.057610034942627 s ( 74.29 )
2024-07-06 03:11:06.171433 INFO::Formatting Data.
2024-07-06 03:11:06.172594 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:06.173959 INFO::Removing potential empty rows and columns
2024-07-06 03:11:06.175575 INFO::Found 0 missing values.
2024-07-06 03:11:06.177436 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.
2024-07-06 03:11:06.185788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:06.186782 INFO::Done
2024-07-06 03:11:06.187682 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:06.192387 INFO::Starting hierarchical adjustment
2024-07-06 03:11:06.193618 INFO::Found 2 batches.
2024-07-06 03:11:06.194728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:06.1958 INFO::Using default BPPARAM
2024-07-06 03:11:06.196611 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:06.19822 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:06.226371 INFO::Done
2024-07-06 03:11:06.227434 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:06.232259 INFO::ASW Batch was 0.681919987888468 prior to batch effect correction and is now -0.0278858800840412 .
2024-07-06 03:11:06.233486 INFO::ASW Label was 0.389751265518873 prior to batch effect correction and is now 0.922184318406418 .
2024-07-06 03:11:06.234788 INFO::Total function execution time is 0.0634067058563232 s and adjustment time is 0.032912015914917 s ( 51.91 )
2024-07-06 03:11:06.23611 INFO::Formatting Data.
2024-07-06 03:11:06.237128 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:06.238748 INFO::Removing potential empty rows and columns
2024-07-06 03:11:06.240632 INFO::Found 0 missing values.
2024-07-06 03:11:06.242234 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.
2024-07-06 03:11:06.250688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:06.251676 INFO::Done
2024-07-06 03:11:06.252527 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:06.257174 INFO::Starting hierarchical adjustment
2024-07-06 03:11:06.258489 INFO::Found 2 batches.
2024-07-06 03:11:06.259433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:06.260389 INFO::Using default BPPARAM
2024-07-06 03:11:06.26125 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:06.262877 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:06.290816 INFO::Done
2024-07-06 03:11:06.291842 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:06.296612 INFO::ASW Batch was 0.681919987888468 prior to batch effect correction and is now -0.0278858800840412 .
2024-07-06 03:11:06.297617 INFO::ASW Label was 0.389751265518873 prior to batch effect correction and is now 0.922184318406418 .
2024-07-06 03:11:06.298945 INFO::Total function execution time is 0.0628013610839844 s and adjustment time is 0.032573938369751 s ( 51.87 )
2024-07-06 03:11:06.659242 INFO::Formatting Data.
2024-07-06 03:11:06.660486 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:06.66199 INFO::Removing potential empty rows and columns
2024-07-06 03:11:06.663746 INFO::Found 0 missing values.
2024-07-06 03:11:06.66867 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:06.669613 INFO::Done
2024-07-06 03:11:06.670405 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:06.673332 INFO::Starting hierarchical adjustment
2024-07-06 03:11:06.67447 INFO::Found 3 batches.
2024-07-06 03:11:06.675282 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:06.67614 INFO::Using default BPPARAM
2024-07-06 03:11:06.676871 INFO::Processing subtree level 1
2024-07-06 03:11:06.820272 INFO::Adjusting the last 1 batches sequentially
2024-07-06 03:11:06.822742 INFO::Done
2024-07-06 03:11:06.823643 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:06.827134 INFO::ASW Batch was -0.0714988539378014 prior to batch effect correction and is now -0.0714988539378014 .
2024-07-06 03:11:06.828609 INFO::Total function execution time is 0.169402122497559 s and adjustment time is 0.148490905761719 s ( 87.66 )
2024-07-06 03:11:06.830233 INFO::Formatting Data.
2024-07-06 03:11:06.831249 INFO::Typecasting input to dataframe.
2024-07-06 03:11:06.832425 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:06.833759 INFO::Removing potential empty rows and columns
2024-07-06 03:11:06.835495 INFO::Found 0 missing values.
2024-07-06 03:11:06.840519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:06.841543 INFO::Done
2024-07-06 03:11:06.842471 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:06.84554 INFO::Starting hierarchical adjustment
2024-07-06 03:11:06.846697 INFO::Found 3 batches.
2024-07-06 03:11:06.847586 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:06.848485 INFO::Using default BPPARAM
2024-07-06 03:11:06.84924 INFO::Processing subtree level 1
2024-07-06 03:11:06.978569 INFO::Adjusting the last 1 batches sequentially
2024-07-06 03:11:06.981236 INFO::Done
2024-07-06 03:11:06.982249 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:06.986057 INFO::ASW Batch was -0.0714988539378014 prior to batch effect correction and is now -0.0714988539378014 .
2024-07-06 03:11:06.987721 INFO::Total function execution time is 0.157441377639771 s and adjustment time is 0.134764909744263 s ( 85.6 )
2024-07-06 03:11:07.009426 INFO::Formatting Data.
2024-07-06 03:11:07.010691 INFO::Typecasting input to dataframe.
2024-07-06 03:11:07.011983 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:07.013359 INFO::Removing potential empty rows and columns
2024-07-06 03:11:07.01524 INFO::Found 0 missing values.
2024-07-06 03:11:07.020726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:07.021711 INFO::Done
2024-07-06 03:11:07.022661 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:07.026042 INFO::Starting hierarchical adjustment
2024-07-06 03:11:07.027333 INFO::Found 3 batches.
2024-07-06 03:11:07.02821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:07.029203 INFO::Using default BPPARAM
2024-07-06 03:11:07.03017 INFO::Processing subtree level 1
2024-07-06 03:11:07.167558 INFO::Adjusting the last 1 batches sequentially
2024-07-06 03:11:07.170031 INFO::Done
2024-07-06 03:11:07.170996 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:07.174487 INFO::ASW Batch was -0.0801115951082305 prior to batch effect correction and is now -0.0801115951082305 .
2024-07-06 03:11:07.175956 INFO::Total function execution time is 0.166583061218262 s and adjustment time is 0.142997026443481 s ( 85.84 )
2024-07-06 03:11:07.401157 INFO::Formatting Data.
2024-07-06 03:11:07.402562 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:07.413624 INFO::Removing potential empty rows and columns
2024-07-06 03:11:07.42124 INFO::Found 1000 missing values.
2024-07-06 03:11:07.456735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:07.45772 INFO::Done
2024-07-06 03:11:07.458641 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:07.470639 INFO::Starting hierarchical adjustment
2024-07-06 03:11:07.47198 INFO::Found 10 batches.
2024-07-06 03:11:07.47285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:07.474166 INFO::Using default BPPARAM
2024-07-06 03:11:07.474939 INFO::Processing subtree level 1
2024-07-06 03:11:07.906678 INFO::Processing subtree level 2
2024-07-06 03:11:08.179498 INFO::Adjusting the last 1 batches sequentially
2024-07-06 03:11:08.182197 INFO::Done
2024-07-06 03:11:08.18311 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:08.191886 INFO::ASW Batch was 0.498776848077772 prior to batch effect correction and is now 0.498776848077772 .
2024-07-06 03:11:08.192863 INFO::ASW Label was 0.307386134188515 prior to batch effect correction and is now 0.307386134188515 .
2024-07-06 03:11:08.194516 INFO::Total function execution time is 0.793386220932007 s and adjustment time is 0.710545778274536 s ( 89.56 )
2024-07-06 03:11:08.19588 INFO::Formatting Data.
2024-07-06 03:11:08.19683 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:08.1989 INFO::Removing potential empty rows and columns
2024-07-06 03:11:08.20459 INFO::Found 1000 missing values.
2024-07-06 03:11:08.241152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:08.242111 INFO::Done
2024-07-06 03:11:08.242864 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:08.251177 INFO::Starting hierarchical adjustment
2024-07-06 03:11:08.252395 INFO::Found 10 batches.
2024-07-06 03:11:09.864836 INFO::Set up parallel execution backend with 2 workers
2024-07-06 03:11:09.866474 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-06 03:11:11.330938 INFO::Adjusting the last 2 batches sequentially
2024-07-06 03:11:11.332824 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-06 03:11:11.357973 INFO::Done
2024-07-06 03:11:11.358815 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:11.365488 INFO::ASW Batch was 0.498776848077772 prior to batch effect correction and is now 0.498776848077772 .
2024-07-06 03:11:11.366315 INFO::ASW Label was 0.307386134188515 prior to batch effect correction and is now 0.307386134188515 .
2024-07-06 03:11:11.367316 INFO::Total function execution time is 3.17152571678162 s and adjustment time is 3.10581851005554 s ( 97.93 )
2024-07-06 03:11:11.558113 INFO::Formatting Data.
2024-07-06 03:11:11.559198 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:11.56042 INFO::Removing potential empty rows and columns
2024-07-06 03:11:11.561975 INFO::Found 0 missing values.
2024-07-06 03:11:11.567718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:11.568507 INFO::Done
2024-07-06 03:11:11.56923 INFO::Acquiring quality metrics before batch effect correction.
2024-07-06 03:11:11.573073 INFO::Starting hierarchical adjustment
2024-07-06 03:11:11.57407 INFO::Found 3 batches.
2024-07-06 03:11:11.574786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-06 03:11:11.575669 INFO::Using default BPPARAM
2024-07-06 03:11:11.576428 INFO::Processing subtree level 1
2024-07-06 03:11:11.712564 INFO::Adjusting the last 1 batches sequentially
2024-07-06 03:11:11.714932 INFO::Done
2024-07-06 03:11:11.715885 INFO::Acquiring quality metrics after batch effect correction.
2024-07-06 03:11:11.720382 INFO::ASW Batch was 0.224791496444693 prior to batch effect correction and is now -0.16058386094024 .
2024-07-06 03:11:11.721279 INFO::ASW Label was -0.19115006045136 prior to batch effect correction and is now -0.0441802754759884 .
2024-07-06 03:11:11.722589 INFO::Total function execution time is 0.164533615112305 s and adjustment time is 0.141083478927612 s ( 85.75 )
2024-07-06 03:11:11.893087 INFO::Formatting Data.
2024-07-06 03:11:11.894137 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:11.895348 INFO::Removing potential empty rows and columns
2024-07-06 03:11:11.896774 INFO::Found 2 missing values.
2024-07-06 03:11:11.900896 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:11.901688 INFO::Done
2024-07-06 03:11:11.94031 INFO::Found NA in Reference column
2024-07-06 03:11:11.953955 INFO::Require at least two references per batch.
2024-07-06 03:11:11.982942 INFO::Formatting Data.
2024-07-06 03:11:11.983891 INFO::Recognized SummarizedExperiment
2024-07-06 03:11:11.984579 INFO::Typecasting input to dataframe.
2024-07-06 03:11:11.998353 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:12.000003 INFO::Removing potential empty rows and columns
2024-07-06 03:11:12.005658 INFO::Found 0 missing values.
2024-07-06 03:11:12.016686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:12.017581 INFO::Done
2024-07-06 03:11:12.039282 INFO::Formatting Data.
2024-07-06 03:11:12.040195 INFO::Recognized SummarizedExperiment
2024-07-06 03:11:12.040987 INFO::Typecasting input to dataframe.
2024-07-06 03:11:12.065791 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:12.067461 INFO::Removing potential empty rows and columns
2024-07-06 03:11:12.073068 INFO::Found 0 missing values.
2024-07-06 03:11:12.091472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:12.09242 INFO::Done
2024-07-06 03:11:12.114463 INFO::Formatting Data.
2024-07-06 03:11:12.115439 INFO::Recognized SummarizedExperiment
2024-07-06 03:11:12.116149 INFO::Typecasting input to dataframe.
2024-07-06 03:11:12.140277 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:12.141628 INFO::Removing potential empty rows and columns
2024-07-06 03:11:12.143147 INFO::Found 0 missing values.
2024-07-06 03:11:12.144363 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.
2024-07-06 03:11:12.151248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:12.152113 INFO::Done
2024-07-06 03:11:12.166603 INFO::Formatting Data.
2024-07-06 03:11:12.167647 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:12.168783 INFO::Removing potential empty rows and columns
2024-07-06 03:11:12.170218 INFO::Found 0 missing values.
2024-07-06 03:11:12.174598 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:12.175431 INFO::Done
2024-07-06 03:11:12.191247 INFO::Formatting Data.
2024-07-06 03:11:12.192364 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:12.193519 INFO::Removing potential empty rows and columns
2024-07-06 03:11:12.194978 INFO::Found 0 missing values.
2024-07-06 03:11:12.199188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:12.199977 INFO::Done
2024-07-06 03:11:12.241299 INFO::Formatting Data.
2024-07-06 03:11:12.242309 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:12.243746 INFO::Removing potential empty rows and columns
2024-07-06 03:11:12.24544 INFO::Found 1 missing values.
2024-07-06 03:11:12.249214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:12.249993 INFO::Done
2024-07-06 03:11:12.276505 INFO::Formatting Data.
2024-07-06 03:11:12.277527 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:12.278685 INFO::Removing potential empty rows and columns
2024-07-06 03:11:12.280066 INFO::Found 2 missing values.
2024-07-06 03:11:12.281312 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.
2024-07-06 03:11:12.284586 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:12.285354 INFO::Done
2024-07-06 03:11:12.299711 INFO::Formatting Data.
2024-07-06 03:11:12.300736 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:12.30202 INFO::Removing potential empty rows and columns
2024-07-06 03:11:12.303306 INFO::Found 2 missing values.
2024-07-06 03:11:12.305538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:12.306282 INFO::Done
2024-07-06 03:11:12.321271 INFO::Formatting Data.
2024-07-06 03:11:12.322324 INFO::Typecasting input to dataframe.
2024-07-06 03:11:12.323447 INFO::Replacing NaNs with NAs.
2024-07-06 03:11:12.324575 INFO::Removing potential empty rows and columns
2024-07-06 03:11:12.325989 INFO::Found 0 missing values.
2024-07-06 03:11:12.330435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-06 03:11:12.331278 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
22.015 5.649 27.015
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.556 | 1.310 | 22.427 | |
| compute_asw | 0.035 | 0.000 | 0.035 | |
| count_existing | 0.02 | 0.00 | 0.02 | |
| generate_data_covariables | 0.017 | 0.000 | 0.017 | |
| generate_dataset | 0.012 | 0.003 | 0.016 | |