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CHECK report for BEclear on merida1

This page was generated on 2020-04-15 12:41:59 -0400 (Wed, 15 Apr 2020).

Package 132/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEclear 2.2.0
David Rasp
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BEclear
Branch: RELEASE_3_10
Last Commit: 0537966
Last Changed Date: 2019-10-29 13:09:18 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BEclear
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BEclear.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BEclear_2.2.0.tar.gz
StartedAt: 2020-04-15 00:38:12 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:39:42 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 90.9 seconds
RetCode: 0
Status:  OK 
CheckDir: BEclear.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BEclear.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BEclear_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/BEclear.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BEclear/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEclear’ version ‘2.2.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
calcBatchEffects 30.829 15.059   7.411
BEclear-package   8.261  4.735   2.282
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/BEclear.Rcheck/00check.log’
for details.



Installation output

BEclear.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BEclear
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘BEclear’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c localLoss.cpp -o localLoss.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BEclear.so RcppExports.o localLoss.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-BEclear/00new/BEclear/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: BEclear
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BEclear)

Tests output

BEclear.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 [2020-04-15 00:39:31] Calculate the batch effects for 2 batches
INFO [2020-04-15 00:39:31] Calculate the batch effects for 3 batches
INFO [2020-04-15 00:39:31] Calculate the batch effects for 3 batches
INFO [2020-04-15 00:39:32] Adjusting p-values
INFO [2020-04-15 00:39:32] Transforming matrix to data.table
INFO [2020-04-15 00:39:32] Calculate the batch effects for 4 batches
INFO [2020-04-15 00:39:32] Adjusting p-values
INFO [2020-04-15 00:39:32] Generating a summary table
INFO [2020-04-15 00:39:32] Calculating the scores for 4 batches
INFO [2020-04-15 00:39:32] Generating a summary table
INFO [2020-04-15 00:39:32] Generating a summary table
INFO [2020-04-15 00:39:33] Transforming matrix to data.table
INFO [2020-04-15 00:39:33] Calculate the batch effects for 3 batches
INFO [2020-04-15 00:39:33] Adjusting p-values
INFO [2020-04-15 00:39:33] Generating a summary table
INFO [2020-04-15 00:39:33] Calculating the scores for 3 batches
INFO [2020-04-15 00:39:33] Removing values with batch effect:
INFO [2020-04-15 00:39:33] 4 values ( 26.6666666666667 % of the data) set to NA
INFO [2020-04-15 00:39:33] Starting the imputation of missing values.
INFO [2020-04-15 00:39:33] This might take a while.
INFO [2020-04-15 00:39:33] BEclear imputation is started:
INFO [2020-04-15 00:39:33] block size: 60  x  60
INFO [2020-04-15 00:39:33] Impute missing data for block 1 of 1
INFO [2020-04-15 00:39:33] Replacing values below 0 or above 1:
INFO [2020-04-15 00:39:33] 0 values replaced
WARN [2020-04-15 00:39:33] 3 values are above 1 or below 0. Check your data
WARN [2020-04-15 00:39:33] Replacing them with missing values
INFO [2020-04-15 00:39:33] Transforming matrix to data.table
INFO [2020-04-15 00:39:33] Calculate the batch effects for 3 batches
INFO [2020-04-15 00:39:33] Adjusting p-values
INFO [2020-04-15 00:39:33] Generating a summary table
INFO [2020-04-15 00:39:33] Calculating the scores for 3 batches
INFO [2020-04-15 00:39:33] Removing values with batch effect:
INFO [2020-04-15 00:39:33] 3 values ( 20 % of the data) set to NA
INFO [2020-04-15 00:39:33] Starting the imputation of missing values.
INFO [2020-04-15 00:39:33] This might take a while.
INFO [2020-04-15 00:39:33] BEclear imputation is started:
INFO [2020-04-15 00:39:33] block size: 60  x  60
INFO [2020-04-15 00:39:33] Impute missing data for block 1 of 1
INFO [2020-04-15 00:39:33] Replacing values below 0 or above 1:
INFO [2020-04-15 00:39:33] 0 values replaced
WARN [2020-04-15 00:39:33] 2 values are above 1 or below 0. Check your data
WARN [2020-04-15 00:39:33] Replacing them with missing values
WARN [2020-04-15 00:39:33] The following samples are annotated in the sample matrix,
WARN [2020-04-15 00:39:33] Dropping those samples now
WARN [2020-04-15 00:39:33] Sample names aren't unique
WARN [2020-04-15 00:39:33] Transforming them to unique IDs. List with annotations will be added to the results
INFO [2020-04-15 00:39:33] Transforming matrix to data.table
INFO [2020-04-15 00:39:33] Calculate the batch effects for 2 batches
INFO [2020-04-15 00:39:33] Adjusting p-values
INFO [2020-04-15 00:39:33] Generating a summary table
INFO [2020-04-15 00:39:33] There were no batch effects detected
INFO [2020-04-15 00:39:33] Starting the imputation of missing values.
INFO [2020-04-15 00:39:33] This might take a while.
INFO [2020-04-15 00:39:33] BEclear imputation is started:
INFO [2020-04-15 00:39:33] block size: 60  x  60
INFO [2020-04-15 00:39:33] Impute missing data for block 1 of 1
INFO [2020-04-15 00:39:33] Replacing values below 0 or above 1:
INFO [2020-04-15 00:39:33] 0 values replaced
INFO [2020-04-15 00:39:33] 3 values outside of the boundaries found
INFO [2020-04-15 00:39:33] Starting the imputation of missing values.
INFO [2020-04-15 00:39:33] This might take a while.
INFO [2020-04-15 00:39:33] BEclear imputation is started:
INFO [2020-04-15 00:39:33] block size: 10  x  10
INFO [2020-04-15 00:39:33] loading futile.logger package
INFO [2020-04-15 00:39:33] Impute missing data for block 1 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 2 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 3 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 4 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 5 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 6 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 7 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 8 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 9 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 10 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 11 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 12 of 25
INFO [2020-04-15 00:39:33] Impute missing data for block 13 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 14 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 15 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 16 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 17 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 18 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 19 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 20 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 21 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 22 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 23 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 24 of 25
INFO [2020-04-15 00:39:34] Impute missing data for block 25 of 25
INFO [2020-04-15 00:39:34] Starting the imputation of missing values.
INFO [2020-04-15 00:39:34] This might take a while.
INFO [2020-04-15 00:39:34] BEclear imputation is started:
INFO [2020-04-15 00:39:34] block size: 0  x  0
INFO [2020-04-15 00:39:34] loading futile.logger package
INFO [2020-04-15 00:39:34] Impute missing data for block 1 of 1
INFO [2020-04-15 00:39:34] Replacing values below 0 or above 1:
INFO [2020-04-15 00:39:34] 3 values replaced
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 83 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.911   8.158   5.888 

Example timings

BEclear.Rcheck/BEclear-Ex.timings

nameusersystemelapsed
BEclear-package8.2614.7352.282
calcBatchEffects30.82915.059 7.411
calcScore1.6761.0500.632
calcSummary0.8440.7500.292
clearBEgenes0.9400.7110.295
correctBatchEffect3.5271.1730.594
countValuesToPredict0.9220.9780.308
findOutsideValues0.9040.3230.694
imputeMissingData1.3361.4100.503
makeBoxplot2.7450.6660.348
preprocessBEclear0.0290.0370.009
replaceOutsideValues0.0690.0880.020