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CHECK report for BEclear on malbec1

This page was generated on 2020-09-21 11:00:57 -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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BEclear.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BEclear_2.5.0.tar.gz
StartedAt: 2020-09-21 02:19:27 -0400 (Mon, 21 Sep 2020)
EndedAt: 2020-09-21 02:20:43 -0400 (Mon, 21 Sep 2020)
EllapsedTime: 76.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BEclear.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BEclear.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BEclear_2.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BEclear.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (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 ‘2.5.0’
* 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 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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
calcBatchEffects 21.504  0.084   9.458
BEclear-package   6.020  0.068   2.893
* 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BEclear.Rcheck/00check.log’
for details.



Installation output

BEclear.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BEclear
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BEclear’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c localLoss.cpp -o localLoss.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o BEclear.so RcppExports.o localLoss.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-BEclear/00new/BEclear/libs
** 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
** 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 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 02:20:37] Calculate the batch effects for 2 batches
INFO [2020-09-21 02:20:37] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:20:37] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:20:37] Adjusting p-values
INFO [2020-09-21 02:20:38] Transforming matrix to data.table
INFO [2020-09-21 02:20:38] Calculate the batch effects for 4 batches
INFO [2020-09-21 02:20:38] Adjusting p-values
INFO [2020-09-21 02:20:38] Generating a summary table
INFO [2020-09-21 02:20:38] Calculating the scores for 4 batches
INFO [2020-09-21 02:20:38] Generating a summary table
INFO [2020-09-21 02:20:38] Generating a summary table
INFO [2020-09-21 02:20:38] Transforming matrix to data.table
INFO [2020-09-21 02:20:38] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:20:38] Adjusting p-values
INFO [2020-09-21 02:20:38] Generating a summary table
INFO [2020-09-21 02:20:38] Calculating the scores for 3 batches
INFO [2020-09-21 02:20:38] Removing values with batch effect:
INFO [2020-09-21 02:20:38] 4 values ( 26.6666666666667 % of the data) set to NA
INFO [2020-09-21 02:20:38] Starting the imputation of missing values.
INFO [2020-09-21 02:20:38] This might take a while.
INFO [2020-09-21 02:20:38] BEclear imputation is started:
INFO [2020-09-21 02:20:38] block size: 60  x  60
INFO [2020-09-21 02:20:38] Impute missing data for block 1 of 1
INFO [2020-09-21 02:20:38] Replacing values below 0 or above 1:
INFO [2020-09-21 02:20:38] 0 values replaced
WARN [2020-09-21 02:20:38] 3 values are above 1 or below 0. Check your data
WARN [2020-09-21 02:20:38] Replacing them with missing values
INFO [2020-09-21 02:20:38] Transforming matrix to data.table
INFO [2020-09-21 02:20:38] Calculate the batch effects for 3 batches
INFO [2020-09-21 02:20:38] Adjusting p-values
INFO [2020-09-21 02:20:38] Generating a summary table
INFO [2020-09-21 02:20:38] Calculating the scores for 3 batches
INFO [2020-09-21 02:20:38] Removing values with batch effect:
INFO [2020-09-21 02:20:38] 3 values ( 20 % of the data) set to NA
INFO [2020-09-21 02:20:38] Starting the imputation of missing values.
INFO [2020-09-21 02:20:38] This might take a while.
INFO [2020-09-21 02:20:38] BEclear imputation is started:
INFO [2020-09-21 02:20:38] block size: 60  x  60
INFO [2020-09-21 02:20:38] Impute missing data for block 1 of 1
INFO [2020-09-21 02:20:38] Replacing values below 0 or above 1:
INFO [2020-09-21 02:20:38] 0 values replaced
WARN [2020-09-21 02:20:38] 2 values are above 1 or below 0. Check your data
WARN [2020-09-21 02:20:38] Replacing them with missing values
WARN [2020-09-21 02:20:38] The following samples are annotated in the sample matrix,
WARN [2020-09-21 02:20:38] Dropping those samples now
WARN [2020-09-21 02:20:38] Sample names aren't unique
WARN [2020-09-21 02:20:38] Transforming them to unique IDs. List with annotations will be added to the results
INFO [2020-09-21 02:20:38] Transforming matrix to data.table
INFO [2020-09-21 02:20:38] Calculate the batch effects for 2 batches
INFO [2020-09-21 02:20:38] Adjusting p-values
INFO [2020-09-21 02:20:38] Generating a summary table
INFO [2020-09-21 02:20:38] There were no batch effects detected
INFO [2020-09-21 02:20:38] Starting the imputation of missing values.
INFO [2020-09-21 02:20:38] This might take a while.
INFO [2020-09-21 02:20:38] BEclear imputation is started:
INFO [2020-09-21 02:20:38] block size: 60  x  60
INFO [2020-09-21 02:20:38] Impute missing data for block 1 of 1
INFO [2020-09-21 02:20:38] Replacing values below 0 or above 1:
INFO [2020-09-21 02:20:38] 0 values replaced
INFO [2020-09-21 02:20:38] 3 values outside of the boundaries found
INFO [2020-09-21 02:20:38] Starting the imputation of missing values.
INFO [2020-09-21 02:20:38] This might take a while.
INFO [2020-09-21 02:20:38] BEclear imputation is started:
INFO [2020-09-21 02:20:38] block size: 10  x  10
INFO [2020-09-21 02:20:38] loading futile.logger package
INFO [2020-09-21 02:20:38] Impute missing data for block 1 of 25
INFO [2020-09-21 02:20:38] Impute missing data for block 2 of 25
INFO [2020-09-21 02:20:38] Impute missing data for block 3 of 25
INFO [2020-09-21 02:20:38] Impute missing data for block 4 of 25
INFO [2020-09-21 02:20:38] Impute missing data for block 5 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 6 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 7 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 8 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 9 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 10 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 11 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 12 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 13 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 14 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 15 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 16 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 17 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 18 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 19 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 20 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 21 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 22 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 23 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 24 of 25
INFO [2020-09-21 02:20:39] Impute missing data for block 25 of 25
INFO [2020-09-21 02:20:39] Starting the imputation of missing values.
INFO [2020-09-21 02:20:39] This might take a while.
INFO [2020-09-21 02:20:39] BEclear imputation is started:
INFO [2020-09-21 02:20:39] block size: 0  x  0
INFO [2020-09-21 02:20:39] loading futile.logger package
INFO [2020-09-21 02:20:39] Impute missing data for block 1 of 1
INFO [2020-09-21 02:20:39] Replacing values below 0 or above 1:
INFO [2020-09-21 02:20:39] 3 values replaced
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 83 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  4.180   0.108   4.268 

Example timings

BEclear.Rcheck/BEclear-Ex.timings

nameusersystemelapsed
BEclear-package6.0200.0682.893
calcBatchEffects21.504 0.084 9.458
calcScore0.3640.0000.338
calcSummary0.2080.0000.190
clearBEgenes0.1920.0040.174
correctBatchEffect0.4720.0040.459
countValuesToPredict0.2080.0000.185
findOutsideValues0.4720.0000.472
imputeMissingData0.3360.0080.322
makeBoxplot0.3280.0040.313
preprocessBEclear0.0040.0000.006
replaceOutsideValues0.0120.0040.019