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CHECK report for banocc on merida2

This page was generated on 2018-10-17 08:58:04 -0400 (Wed, 17 Oct 2018).

Package 91/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
banocc 1.4.0
Emma Schwager
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/banocc
Branch: RELEASE_3_7
Last Commit: d937c6d
Last Changed Date: 2018-04-30 10:35:46 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: banocc
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:banocc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings banocc_1.4.0.tar.gz
StartedAt: 2018-10-16 19:58:47 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:00:53 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 125.8 seconds
RetCode: 0
Status:  OK 
CheckDir: banocc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:banocc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings banocc_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/banocc.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 ‘banocc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘banocc’ version ‘1.4.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘banocc’ 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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calc_snc: no visible global function definition for ‘sd’
get_IVs : <anonymous>: no visible global function definition for
  ‘rgamma’
get_banocc_output : <anonymous>: no visible global function definition
  for ‘cov2cor’
get_posterior_quantiles: no visible binding for global variable
  ‘quantile’
rgbeta: no visible global function definition for ‘rbeta’
rgbeta: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  cov2cor quantile rbeta rbinom rgamma sd
Consider adding
  importFrom("stats", "cov2cor", "quantile", "rbeta", "rbinom", "rgamma",
             "sd")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/banocc.Rcheck/00check.log’
for details.



Installation output

banocc.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘banocc’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (banocc)

Tests output

banocc.Rcheck/tests/testthat.Rout


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(banocc)
Loading required package: rstan
Loading required package: ggplot2
Loading required package: StanHeaders
rstan (Version 2.18.1, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
> 
> test_check("banocc")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 2616 SKIPPED: 7 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 79.326   2.936  82.980 

Example timings

banocc.Rcheck/banocc-Ex.timings

nameusersystemelapsed
banocc_model0.0140.0010.015
get_banocc_output0.0160.0010.018
run_banocc0.0170.0020.018