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BioC 3.5: CHECK report for pint on veracruz2

This page was generated on 2017-10-18 14:28:59 -0400 (Wed, 18 Oct 2017).

Package 986/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pint 1.26.0
Olli-Pekka Huovilainen
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/pint
Branch: RELEASE_3_5
Last Commit: b86cffb
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pint
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pint_1.26.0.tar.gz
StartedAt: 2017-10-18 07:20:10 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 07:22:32 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 142.0 seconds
RetCode: 0
Status:  OK 
CheckDir: pint.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pint_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/pint.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pint/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pint’ version ‘1.26.0’
* 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 ‘pint’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Matrix’ ‘methods’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
W.effects: no visible global function definition for ‘princomp’
W.effects: no visible global function definition for ‘cor’
calculate.arm: no visible global function definition for ‘as’
calculate.arm: no visible global function definition for ‘new’
calculate.arm.sparse: no visible global function definition for ‘new’
calculate.chr: no visible global function definition for ‘new’
calculate.chr.sparse: no visible global function definition for ‘new’
calculate.genome: no visible global function definition for ‘new’
calculate.genome.sparse: no visible global function definition for
  ‘new’
imputation: no visible global function definition for ‘rnorm’
imputation: no visible global function definition for ‘sd’
join.top.regions: no visible global function definition for ‘quantile’
plot.ChromosomeModels: no visible global function definition for ‘par’
plot.ChromosomeModels: no visible global function definition for
  ‘abline’
plot.ChromosomeModels: no visible global function definition for
  ‘points’
plot.ChromosomeModels: no visible global function definition for ‘text’
plot.ChromosomeModels: no visible global function definition for
  ‘lines’
plot.GeneDependencyModel: no visible global function definition for
  ‘gray’
plot.GeneDependencyModel: no visible global function definition for
  ‘par’
plot.GeneDependencyModel: no visible global function definition for
  ‘layout’
plot.GeneDependencyModel: no visible global function definition for
  ‘barplot’
plot.GeneDependencyModel: no visible global function definition for
  ‘legend’
plot.GeneDependencyModel: no visible global function definition for
  ‘mtext’
plot.GenomeModels: no visible global function definition for ‘par’
plot.GenomeModels: no visible global function definition for ‘abline’
plot.GenomeModels: no visible global function definition for ‘points’
plot.GenomeModels: no visible global function definition for ‘text’
plot.GenomeModels: no visible global function definition for ‘lines’
plot.GenomeModels: no visible global function definition for ‘axis’
summarize.region.parameters: no visible global function definition for
  ‘na.omit’
summarize.region.parameters: no visible global function definition for
  ‘cor’
z.effects: no visible global function definition for ‘princomp’
coerce,GeneDependencyModel-DependencyModel: no visible global function
  definition for ‘new’
coerce<-,GeneDependencyModel-DependencyModel: no visible global
  function definition for ‘slot<-’
coerce<-,GeneDependencyModel-DependencyModel: no visible global
  function definition for ‘slot’
getPArm,ChromosomeModels: no visible global function definition for
  ‘new’
getQArm,ChromosomeModels: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  abline as axis barplot cor gray layout legend lines mtext na.omit new
  par points princomp quantile rnorm sd slot slot<- text
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "barplot", "layout", "legend",
             "lines", "mtext", "par", "points", "text")
  importFrom("methods", "as", "new", "slot", "slot<-")
  importFrom("stats", "cor", "na.omit", "princomp", "quantile", "rnorm",
             "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
screen                    34.987  0.457  36.677
ChromosomeModels-class    28.834  0.471  30.229
plot                       9.001  0.086   9.311
GeneDependencyModel-class  7.931  0.086   8.269
* 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-3.5-bioc/meat/pint.Rcheck/00check.log’
for details.


pint.Rcheck/00install.out:

* installing *source* package ‘pint’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pint)

pint.Rcheck/pint-Ex.timings:

nameusersystemelapsed
ChromosomeModels-class28.834 0.47130.229
GeneDependencyModel-class7.9310.0868.269
fit.byname0.0880.0030.096
get.neighboring.probes0.0010.0000.001
get.neighs0.0000.0000.001
join.top.regions0.0000.0000.001
order.feature.info0.0010.0010.001
pint.data0.0970.0010.102
plot9.0010.0869.311
screen34.987 0.45736.677
summarize.region.parameters0.0010.0000.001
window0.1110.0020.116
z.effect0.0810.0030.088