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CHECK report for CAFE on veracruz1

This page was generated on 2018-04-12 13:38:14 -0400 (Thu, 12 Apr 2018).

Package 170/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAFE 1.14.0
Sander Bollen
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CAFE
Branch: RELEASE_3_6
Last Commit: faeadcc
Last Changed Date: 2017-10-30 12:40:12 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CAFE
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAFE_1.14.0.tar.gz
StartedAt: 2018-04-12 01:12:17 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:17:15 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 298.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CAFE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAFE_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CAFE.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAFE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAFE’ version ‘1.14.0’
* 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 ‘CAFE’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... 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
Armchisqr: no visible global function definition for 'chisq.test'
ArmfisherExact: no visible global function definition for 'fisher.test'
ProcessCels: no visible global function definition for 'download.file'
ProcessCels: no visible global function definition for 'read.table'
ProcessCels: no visible global function definition for 'txtProgressBar'
ProcessCels: no visible global function definition for
  'setTxtProgressBar'
ProcessCels: no visible global function definition for 'na.omit'
allBandsOnChrom: no visible global function definition for
  'fisher.test'
allBandsOnChromChi: no visible global function definition for
  'chisq.test'
armStats: no visible global function definition for 'p.adjust'
bandStats: no visible global function definition for 'p.adjust'
chisqr: no visible global function definition for 'chisq.test'
chromosomeStats: no visible global function definition for 'p.adjust'
discontPlot: no visible global function definition for 'png'
discontPlot: no visible global function definition for 'dev.off'
discontPlot: no visible global function definition for 'data'
facetPlot: no visible global function definition for 'png'
facetPlot: no visible global function definition for 'dev.off'
facetPlot: no visible global function definition for 'na.omit'
fisher.method: no visible global function definition for 'pchisq'
fisherExact: no visible global function definition for 'fisher.test'
makelevels: no visible global function definition for 'na.omit'
rawPlot: no visible global function definition for 'png'
rawPlot: no visible global function definition for 'dev.off'
rawPlot: no visible global function definition for 'data'
slidPlot: no visible global function definition for 'png'
slidPlot: no visible global function definition for 'dev.off'
slidPlot: no visible global function definition for 'data'
Undefined global functions or variables:
  chisq.test data dev.off download.file fisher.test na.omit p.adjust
  pchisq png read.table setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("stats", "chisq.test", "fisher.test", "na.omit", "p.adjust",
             "pchisq")
  importFrom("utils", "data", "download.file", "read.table",
             "setTxtProgressBar", "txtProgressBar")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
facetPlot 5.996  0.389   6.514
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/CAFE.Rcheck/00check.log’
for details.



Installation output

CAFE.Rcheck/00install.out

* installing *source* package ‘CAFE’ ...
** R
** data
** inst
** 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 (CAFE)

Tests output

CAFE.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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.

> #BiocGenerics:::testPackage("CAFE")
> 
> proc.time()
   user  system elapsed 
  0.210   0.038   0.235 

Example timings

CAFE.Rcheck/CAFE-Ex.timings

nameusersystemelapsed
CAFE-package0.0010.0010.002
CAFE0.6020.0250.634
ProcessCels0.0000.0000.001
armStats1.5350.0501.601
bandStats1.6310.0611.704
chromosomeStats0.5610.0140.579
cliSubset0.0000.0000.001
discontPlot3.1680.2873.464
discontSmooth0.0080.0010.008
facetPlot5.9960.3896.514
fisher.method0.0010.0000.001
guiSubset0.0000.0000.001
rawPlot1.1440.0491.198
slidPlot2.4780.0962.608
slidSmooth0.0020.0000.003