Package: bigmemoryExtras

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bigmemoryExtras.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bigmemoryExtras_1.28.0.tar.gz

StartedAt: 2018-10-16 20:04:43 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:05:14 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 31.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: bigmemoryExtras.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bigmemoryExtras.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bigmemoryExtras_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/bigmemoryExtras.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bigmemoryExtras/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bigmemoryExtras’ version ‘1.28.0’
* 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:
  .BBSoptions
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 ‘bigmemoryExtras’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 ... WARNING
'::' or ':::' import not declared from: ‘biganalytics’
'library' or 'require' call not declared from: ‘biganalytics’
'library' or 'require' call to ‘biganalytics’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘bigmemoryExtras/R/collections.R’:
  unlockBinding(item, x)
* 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘bigmemoryExtras.Rmd’
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/bigmemoryExtras.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/bigmemoryExtras.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bigmemoryExtras
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘bigmemoryExtras’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘apply’ from package ‘base’ in package ‘bigmemoryExtras’
Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘bigmemoryExtras’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bigmemoryExtras)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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(bigmemoryExtras)
Loading required package: bigmemory
> 
> test_check("bigmemoryExtras")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 63 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  2.072   0.136   2.212 

name	user	system	elapsed
BigMatrix-class	0.199	0.011	0.222
BigMatrix	0.072	0.001	0.076
BigMatrixFactor-class	0.064	0.001	0.066
BigMatrixFactor	0.060	0.001	0.062
updateBackingfiles	0.001	0.000	0.001