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CHECK report for BEclear on merida1

This page was generated on 2021-04-17 12:10:15 -0400 (Sat, 17 Apr 2021).

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 139/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEclear 2.6.0  (landing page)
David Rasp
Snapshot Date: 2021-04-16 14:50:12 -0400 (Fri, 16 Apr 2021)
URL: https://git.bioconductor.org/packages/BEclear
Branch: RELEASE_3_12
Last Commit: c0d806a
Last Changed Date: 2020-10-27 11:05:28 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: BEclear
Version: 2.6.0
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_2.6.0.tar.gz
StartedAt: 2021-04-16 23:03:38 -0400 (Fri, 16 Apr 2021)
EndedAt: 2021-04-16 23:06:18 -0400 (Fri, 16 Apr 2021)
EllapsedTime: 160.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BEclear.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BEclear.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.6.0’
* 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 54.445  0.192  54.741
BEclear-package  12.355  0.070  12.449
* 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/BEclear.Rcheck/00check.log’
for details.



Installation output

BEclear.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BEclear’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c localLoss.cpp -o localLoss.o
In file included from localLoss.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/4.0/Resources/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 [2021-04-16 23:06:05] Calculate the batch effects for 2 batches
INFO [2021-04-16 23:06:05] Calculate the batch effects for 3 batches
INFO [2021-04-16 23:06:05] Calculate the batch effects for 3 batches
INFO [2021-04-16 23:06:05] Adjusting p-values
INFO [2021-04-16 23:06:05] Transforming matrix to data.table
INFO [2021-04-16 23:06:05] Calculate the batch effects for 4 batches
INFO [2021-04-16 23:06:07] Adjusting p-values
INFO [2021-04-16 23:06:07] Generating a summary table
INFO [2021-04-16 23:06:07] Calculating the scores for 4 batches
INFO [2021-04-16 23:06:07] Generating a summary table
INFO [2021-04-16 23:06:07] Generating a summary table
INFO [2021-04-16 23:06:07] Transforming matrix to data.table
INFO [2021-04-16 23:06:07] Calculate the batch effects for 3 batches
INFO [2021-04-16 23:06:08] Adjusting p-values
INFO [2021-04-16 23:06:08] Generating a summary table
INFO [2021-04-16 23:06:08] Calculating the scores for 3 batches
INFO [2021-04-16 23:06:08] Removing values with batch effect:
INFO [2021-04-16 23:06:08] 4 values ( 26.6666666666667 % of the data) set to NA
INFO [2021-04-16 23:06:08] Starting the imputation of missing values.
INFO [2021-04-16 23:06:08] This might take a while.
INFO [2021-04-16 23:06:08] BEclear imputation is started:
INFO [2021-04-16 23:06:08] block size: 60  x  60
INFO [2021-04-16 23:06:08] Impute missing data for block 1 of 1
INFO [2021-04-16 23:06:08] Replacing values below 0 or above 1:
INFO [2021-04-16 23:06:08] 0 values replaced
WARN [2021-04-16 23:06:08] 3 values are above 1 or below 0. Check your data
WARN [2021-04-16 23:06:08] Replacing them with missing values
INFO [2021-04-16 23:06:08] Transforming matrix to data.table
INFO [2021-04-16 23:06:08] Calculate the batch effects for 3 batches
INFO [2021-04-16 23:06:08] Adjusting p-values
INFO [2021-04-16 23:06:08] Generating a summary table
INFO [2021-04-16 23:06:08] Calculating the scores for 3 batches
INFO [2021-04-16 23:06:08] Removing values with batch effect:
INFO [2021-04-16 23:06:08] 3 values ( 20 % of the data) set to NA
INFO [2021-04-16 23:06:08] Starting the imputation of missing values.
INFO [2021-04-16 23:06:08] This might take a while.
INFO [2021-04-16 23:06:08] BEclear imputation is started:
INFO [2021-04-16 23:06:08] block size: 60  x  60
INFO [2021-04-16 23:06:08] Impute missing data for block 1 of 1
INFO [2021-04-16 23:06:08] Replacing values below 0 or above 1:
INFO [2021-04-16 23:06:08] 0 values replaced
WARN [2021-04-16 23:06:08] 2 values are above 1 or below 0. Check your data
WARN [2021-04-16 23:06:08] Replacing them with missing values
WARN [2021-04-16 23:06:08] The following samples are annotated in the sample matrix,
WARN [2021-04-16 23:06:08] Dropping those samples now
WARN [2021-04-16 23:06:08] Sample names aren't unique
WARN [2021-04-16 23:06:08] Transforming them to unique IDs. List with annotations will be added to the results
INFO [2021-04-16 23:06:08] Transforming matrix to data.table
INFO [2021-04-16 23:06:08] Calculate the batch effects for 2 batches
INFO [2021-04-16 23:06:08] Adjusting p-values
INFO [2021-04-16 23:06:08] Generating a summary table
INFO [2021-04-16 23:06:08] There were no batch effects detected
INFO [2021-04-16 23:06:08] Starting the imputation of missing values.
INFO [2021-04-16 23:06:08] This might take a while.
INFO [2021-04-16 23:06:08] BEclear imputation is started:
INFO [2021-04-16 23:06:08] block size: 60  x  60
INFO [2021-04-16 23:06:08] Impute missing data for block 1 of 1
INFO [2021-04-16 23:06:08] Replacing values below 0 or above 1:
INFO [2021-04-16 23:06:08] 0 values replaced
INFO [2021-04-16 23:06:08] 3 values outside of the boundaries found
INFO [2021-04-16 23:06:08] Starting the imputation of missing values.
INFO [2021-04-16 23:06:08] This might take a while.
INFO [2021-04-16 23:06:08] BEclear imputation is started:
INFO [2021-04-16 23:06:08] block size: 10  x  10
INFO [2021-04-16 23:06:08] loading futile.logger package
INFO [2021-04-16 23:06:08] Impute missing data for block 1 of 25
INFO [2021-04-16 23:06:08] Impute missing data for block 2 of 25
INFO [2021-04-16 23:06:08] Impute missing data for block 3 of 25
INFO [2021-04-16 23:06:08] Impute missing data for block 4 of 25
INFO [2021-04-16 23:06:08] Impute missing data for block 5 of 25
INFO [2021-04-16 23:06:08] Impute missing data for block 6 of 25
INFO [2021-04-16 23:06:08] Impute missing data for block 7 of 25
INFO [2021-04-16 23:06:08] Impute missing data for block 8 of 25
INFO [2021-04-16 23:06:08] Impute missing data for block 9 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 10 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 11 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 12 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 13 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 14 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 15 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 16 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 17 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 18 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 19 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 20 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 21 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 22 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 23 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 24 of 25
INFO [2021-04-16 23:06:09] Impute missing data for block 25 of 25
INFO [2021-04-16 23:06:09] Starting the imputation of missing values.
INFO [2021-04-16 23:06:09] This might take a while.
INFO [2021-04-16 23:06:09] BEclear imputation is started:
INFO [2021-04-16 23:06:09] block size: 0  x  0
INFO [2021-04-16 23:06:09] loading futile.logger package
INFO [2021-04-16 23:06:09] Impute missing data for block 1 of 1
INFO [2021-04-16 23:06:09] Replacing values below 0 or above 1:
INFO [2021-04-16 23:06:09] 3 values replaced
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 83 ]
> 
> proc.time()
   user  system elapsed 
  7.325   0.285   7.781 

Example timings

BEclear.Rcheck/BEclear-Ex.timings

nameusersystemelapsed
BEclear-package12.355 0.07012.449
calcBatchEffects54.445 0.19254.741
calcScore1.5140.0071.523
calcSummary1.3960.0071.405
clearBEgenes1.4840.0061.493
correctBatchEffect1.6410.0171.659
countValuesToPredict1.4790.0061.486
findOutsideValues0.590.010.60
imputeMissingData1.4750.0121.489
makeBoxplot1.3950.0071.404
preprocessBEclear0.0050.0010.006
replaceOutsideValues0.0150.0020.017