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CHECK report for BEclear on tokay1

This page was generated on 2020-09-21 11:13:44 -0400 (Mon, 21 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BEclear PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 132/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEclear 2.5.0
David Rasp
Snapshot Date: 2020-09-20 14:41:51 -0400 (Sun, 20 Sep 2020)
URL: https://git.bioconductor.org/packages/BEclear
Branch: master
Last Commit: 89d633c
Last Changed Date: 2020-05-05 03:54:26 -0400 (Tue, 05 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BEclear
Version: 2.5.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEclear.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BEclear_2.5.0.tar.gz
StartedAt: 2020-09-21 02:38:50 -0400 (Mon, 21 Sep 2020)
EndedAt: 2020-09-21 02:40:54 -0400 (Mon, 21 Sep 2020)
EllapsedTime: 123.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BEclear.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEclear.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BEclear_2.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BEclear.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BEclear/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BEclear' version '2.5.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'BEclear' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... WARNING
prepare_Rd: x:1: unexpected END_OF_INPUT '%} confidence level}'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BEclear/libs/i386/BEclear.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BEclear/libs/x64/BEclear.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
calcBatchEffects 5.61   0.11    5.71
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BEclear.Rcheck/00check.log'
for details.



Installation output

BEclear.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BEclear_2.5.0.tar.gz && rm -rf BEclear.buildbin-libdir && mkdir BEclear.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BEclear.buildbin-libdir BEclear_2.5.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BEclear_2.5.0.zip && rm BEclear_2.5.0.tar.gz BEclear_2.5.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  210k  100  210k    0     0  5684k      0 --:--:-- --:--:-- --:--:-- 6378k

install for i386

* installing *source* package 'BEclear' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c localLoss.cpp -o localLoss.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o BEclear.dll tmp.def RcppExports.o localLoss.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BEclear.buildbin-libdir/00LOCK-BEclear/00new/BEclear/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: BEclear
Warning in tools::parseLatex(x) :
  x:1: unexpected END_OF_INPUT '%} confidence level}'
*** installing help indices
  converting help for package 'BEclear'
    finding HTML links ... done
    BEclear-example-methylation-data        html  
    BEclear-example-sample-data             html  
    BEclear-package                         html  
    calcBatchEffects                        html  
    calcBatchEffectsForBatch                html  
    calcBlockFrame                          html  
    calcPositions                           html  
    calcScore                               html  
    calcSummary                             html  
    clearBEgenes                            html  
    combineBlocks                           html  
    correctBatchEffect                      html  
    countValuesToPredict                    html  
    ex.corrected.data                       html  
    findOutsideValues                       html  
    gdepoch                                 html  
    imputeMissingData                       html  
    imputeMissingDataForBlock               html  
    localLoss                               html  
    loss                                    html  
    makeBoxplot                             html  
    preprocessBEclear                       html  
    replaceOutsideValues                    html  
    runGradientDescent                      html  
** 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

install for x64

* installing *source* package 'BEclear' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c localLoss.cpp -o localLoss.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BEclear.dll tmp.def RcppExports.o localLoss.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BEclear.buildbin-libdir/BEclear/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BEclear' as BEclear_2.5.0.zip
* DONE (BEclear)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BEclear' successfully unpacked and MD5 sums checked

Tests output

BEclear.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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.

> library(testthat)
> library(BEclear)
Loading required package: BiocParallel
> 
> test_check("BEclear")
INFO [2020-09-21 02:40:37] Calculate the batch effects for 2 batches
INFO [2020-09-21 02:40:37] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:40:37] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:40:37] Adjusting p-values
INFO [2020-09-21 02:40:38] Transforming matrix to data.table
INFO [2020-09-21 02:40:38] Calculate the batch effects for 4 batches
INFO [2020-09-21 02:40:38] Adjusting p-values
INFO [2020-09-21 02:40:38] Generating a summary table
INFO [2020-09-21 02:40:38] Calculating the scores for 4 batches
INFO [2020-09-21 02:40:38] Generating a summary table
INFO [2020-09-21 02:40:38] Generating a summary table
INFO [2020-09-21 02:40:38] Transforming matrix to data.table
INFO [2020-09-21 02:40:38] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:40:38] Adjusting p-values
INFO [2020-09-21 02:40:38] Generating a summary table
INFO [2020-09-21 02:40:38] Calculating the scores for 3 batches
INFO [2020-09-21 02:40:38] Removing values with batch effect:
INFO [2020-09-21 02:40:38] 4 values ( 26.6666666666667 % of the data) set to NA
INFO [2020-09-21 02:40:38] Starting the imputation of missing values.
INFO [2020-09-21 02:40:38] This might take a while.
INFO [2020-09-21 02:40:38] BEclear imputation is started:
INFO [2020-09-21 02:40:38] block size: 60  x  60
INFO [2020-09-21 02:40:38] Impute missing data for block 1 of 1
INFO [2020-09-21 02:40:38] Replacing values below 0 or above 1:
INFO [2020-09-21 02:40:38] 0 values replaced
WARN [2020-09-21 02:40:38] 3 values are above 1 or below 0. Check your data
WARN [2020-09-21 02:40:38] Replacing them with missing values
INFO [2020-09-21 02:40:38] Transforming matrix to data.table
INFO [2020-09-21 02:40:38] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:40:38] Adjusting p-values
INFO [2020-09-21 02:40:38] Generating a summary table
INFO [2020-09-21 02:40:38] Calculating the scores for 3 batches
INFO [2020-09-21 02:40:38] Removing values with batch effect:
INFO [2020-09-21 02:40:38] 3 values ( 20 % of the data) set to NA
INFO [2020-09-21 02:40:38] Starting the imputation of missing values.
INFO [2020-09-21 02:40:38] This might take a while.
INFO [2020-09-21 02:40:38] BEclear imputation is started:
INFO [2020-09-21 02:40:38] block size: 60  x  60
INFO [2020-09-21 02:40:38] Impute missing data for block 1 of 1
INFO [2020-09-21 02:40:38] Replacing values below 0 or above 1:
INFO [2020-09-21 02:40:38] 0 values replaced
WARN [2020-09-21 02:40:38] 2 values are above 1 or below 0. Check your data
WARN [2020-09-21 02:40:38] Replacing them with missing values
WARN [2020-09-21 02:40:38] The following samples are annotated in the sample matrix,
WARN [2020-09-21 02:40:38] Dropping those samples now
WARN [2020-09-21 02:40:38] Sample names aren't unique
WARN [2020-09-21 02:40:38] Transforming them to unique IDs. List with annotations will be added to the results
INFO [2020-09-21 02:40:38] Transforming matrix to data.table
INFO [2020-09-21 02:40:38] Calculate the batch effects for 2 batches
INFO [2020-09-21 02:40:38] Adjusting p-values
INFO [2020-09-21 02:40:38] Generating a summary table
INFO [2020-09-21 02:40:38] There were no batch effects detected
INFO [2020-09-21 02:40:38] Starting the imputation of missing values.
INFO [2020-09-21 02:40:38] This might take a while.
INFO [2020-09-21 02:40:38] BEclear imputation is started:
INFO [2020-09-21 02:40:38] block size: 60  x  60
INFO [2020-09-21 02:40:38] Impute missing data for block 1 of 1
INFO [2020-09-21 02:40:38] Replacing values below 0 or above 1:
INFO [2020-09-21 02:40:38] 0 values replaced
INFO [2020-09-21 02:40:38] 3 values outside of the boundaries found
INFO [2020-09-21 02:40:38] Starting the imputation of missing values.
INFO [2020-09-21 02:40:38] This might take a while.
INFO [2020-09-21 02:40:38] BEclear imputation is started:
INFO [2020-09-21 02:40:38] block size: 10  x  10
INFO [2020-09-21 02:40:38] loading futile.logger package
INFO [2020-09-21 02:40:38] Impute missing data for block 1 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 2 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 3 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 4 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 5 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 6 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 7 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 8 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 9 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 10 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 11 of 25
INFO [2020-09-21 02:40:38] Impute missing data for block 12 of 25
INFO [2020-09-21 02:40:39] Impute missing data for block 13 of 25
INFO [2020-09-21 02:40:39] Impute missing data for block 14 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 15 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 16 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 17 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 18 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 19 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 20 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 21 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 22 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 23 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 24 of 25
INFO [2020-09-21 02:40:42] Impute missing data for block 25 of 25
INFO [2020-09-21 02:40:42] Starting the imputation of missing values.
INFO [2020-09-21 02:40:42] This might take a while.
INFO [2020-09-21 02:40:42] BEclear imputation is started:
INFO [2020-09-21 02:40:42] block size: 0  x  0
INFO [2020-09-21 02:40:42] loading futile.logger package
INFO [2020-09-21 02:40:42] Impute missing data for block 1 of 1
INFO [2020-09-21 02:40:42] Replacing values below 0 or above 1:
INFO [2020-09-21 02:40:42] 3 values replaced
== testthat results  ===========================================================
[ OK: 83 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   3.95    0.25    7.29 

BEclear.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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.

> library(testthat)
> library(BEclear)
Loading required package: BiocParallel
> 
> test_check("BEclear")
INFO [2020-09-21 02:40:46] Calculate the batch effects for 2 batches
INFO [2020-09-21 02:40:47] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:40:47] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:40:47] Adjusting p-values
INFO [2020-09-21 02:40:47] Transforming matrix to data.table
INFO [2020-09-21 02:40:47] Calculate the batch effects for 4 batches
INFO [2020-09-21 02:40:47] Adjusting p-values
INFO [2020-09-21 02:40:47] Generating a summary table
INFO [2020-09-21 02:40:47] Calculating the scores for 4 batches
INFO [2020-09-21 02:40:47] Generating a summary table
INFO [2020-09-21 02:40:47] Generating a summary table
INFO [2020-09-21 02:40:47] Transforming matrix to data.table
INFO [2020-09-21 02:40:47] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:40:47] Adjusting p-values
INFO [2020-09-21 02:40:47] Generating a summary table
INFO [2020-09-21 02:40:48] Calculating the scores for 3 batches
INFO [2020-09-21 02:40:48] Removing values with batch effect:
INFO [2020-09-21 02:40:48] 4 values ( 26.6666666666667 % of the data) set to NA
INFO [2020-09-21 02:40:48] Starting the imputation of missing values.
INFO [2020-09-21 02:40:48] This might take a while.
INFO [2020-09-21 02:40:48] BEclear imputation is started:
INFO [2020-09-21 02:40:48] block size: 60  x  60
INFO [2020-09-21 02:40:48] Impute missing data for block 1 of 1
INFO [2020-09-21 02:40:48] Replacing values below 0 or above 1:
INFO [2020-09-21 02:40:48] 0 values replaced
WARN [2020-09-21 02:40:48] 3 values are above 1 or below 0. Check your data
WARN [2020-09-21 02:40:48] Replacing them with missing values
INFO [2020-09-21 02:40:48] Transforming matrix to data.table
INFO [2020-09-21 02:40:48] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:40:48] Adjusting p-values
INFO [2020-09-21 02:40:48] Generating a summary table
INFO [2020-09-21 02:40:48] Calculating the scores for 3 batches
INFO [2020-09-21 02:40:48] Removing values with batch effect:
INFO [2020-09-21 02:40:48] 3 values ( 20 % of the data) set to NA
INFO [2020-09-21 02:40:48] Starting the imputation of missing values.
INFO [2020-09-21 02:40:48] This might take a while.
INFO [2020-09-21 02:40:48] BEclear imputation is started:
INFO [2020-09-21 02:40:48] block size: 60  x  60
INFO [2020-09-21 02:40:48] Impute missing data for block 1 of 1
INFO [2020-09-21 02:40:48] Replacing values below 0 or above 1:
INFO [2020-09-21 02:40:48] 0 values replaced
WARN [2020-09-21 02:40:48] 2 values are above 1 or below 0. Check your data
WARN [2020-09-21 02:40:48] Replacing them with missing values
WARN [2020-09-21 02:40:48] The following samples are annotated in the sample matrix,
WARN [2020-09-21 02:40:48] Dropping those samples now
WARN [2020-09-21 02:40:48] Sample names aren't unique
WARN [2020-09-21 02:40:48] Transforming them to unique IDs. List with annotations will be added to the results
INFO [2020-09-21 02:40:48] Transforming matrix to data.table
INFO [2020-09-21 02:40:48] Calculate the batch effects for 2 batches
INFO [2020-09-21 02:40:48] Adjusting p-values
INFO [2020-09-21 02:40:48] Generating a summary table
INFO [2020-09-21 02:40:48] There were no batch effects detected
INFO [2020-09-21 02:40:48] Starting the imputation of missing values.
INFO [2020-09-21 02:40:48] This might take a while.
INFO [2020-09-21 02:40:48] BEclear imputation is started:
INFO [2020-09-21 02:40:48] block size: 60  x  60
INFO [2020-09-21 02:40:48] Impute missing data for block 1 of 1
INFO [2020-09-21 02:40:48] Replacing values below 0 or above 1:
INFO [2020-09-21 02:40:48] 0 values replaced
INFO [2020-09-21 02:40:48] 3 values outside of the boundaries found
INFO [2020-09-21 02:40:48] Starting the imputation of missing values.
INFO [2020-09-21 02:40:48] This might take a while.
INFO [2020-09-21 02:40:48] BEclear imputation is started:
INFO [2020-09-21 02:40:48] block size: 10  x  10
INFO [2020-09-21 02:40:48] loading futile.logger package
INFO [2020-09-21 02:40:48] Impute missing data for block 1 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 2 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 3 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 4 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 5 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 6 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 7 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 8 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 9 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 10 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 11 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 12 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 13 of 25
INFO [2020-09-21 02:40:48] Impute missing data for block 14 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 15 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 16 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 17 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 18 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 19 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 20 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 21 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 22 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 23 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 24 of 25
INFO [2020-09-21 02:40:49] Impute missing data for block 25 of 25
INFO [2020-09-21 02:40:49] Starting the imputation of missing values.
INFO [2020-09-21 02:40:49] This might take a while.
INFO [2020-09-21 02:40:49] BEclear imputation is started:
INFO [2020-09-21 02:40:49] block size: 0  x  0
INFO [2020-09-21 02:40:49] loading futile.logger package
INFO [2020-09-21 02:40:49] Impute missing data for block 1 of 1
INFO [2020-09-21 02:40:49] Replacing values below 0 or above 1:
INFO [2020-09-21 02:40:49] 3 values replaced
== testthat results  ===========================================================
[ OK: 83 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   6.25    0.26    6.57 

Example timings

BEclear.Rcheck/examples_i386/BEclear-Ex.timings

nameusersystemelapsed
BEclear-package1.720.031.74
calcBatchEffects5.610.115.71
calcScore0.280.000.28
calcSummary0.230.030.26
clearBEgenes0.270.020.28
correctBatchEffect0.520.010.99
countValuesToPredict0.280.000.28
findOutsideValues0.480.000.48
imputeMissingData0.280.020.30
makeBoxplot0.210.000.20
preprocessBEclear0.000.010.02
replaceOutsideValues0.010.000.01

BEclear.Rcheck/examples_x64/BEclear-Ex.timings

nameusersystemelapsed
BEclear-package1.310.031.34
calcBatchEffects4.470.244.42
calcScore0.210.000.20
calcSummary0.180.000.19
clearBEgenes0.190.000.19
correctBatchEffect0.330.010.42
countValuesToPredict0.170.020.19
findOutsideValues0.310.000.31
imputeMissingData0.270.050.31
makeBoxplot0.210.030.23
preprocessBEclear0.020.000.02
replaceOutsideValues0.020.000.01