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CHECK report for pint on malbec2

This page was generated on 2018-10-17 08:22:59 -0400 (Wed, 17 Oct 2018).

Package 1099/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pint 1.30.0
Olli-Pekka Huovilainen
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/pint
Branch: RELEASE_3_7
Last Commit: 74156ad
Last Changed Date: 2018-04-30 10:35:12 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pint
Version: 1.30.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pint.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pint_1.30.0.tar.gz
StartedAt: 2018-10-16 02:43:46 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:45:24 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 98.1 seconds
RetCode: 0
Status:  OK 
CheckDir: pint.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pint.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pint_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/pint.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.30.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
screen                    23.588  0.020  23.628
ChromosomeModels-class    21.600  0.020  21.631
plot                       5.892  0.004   5.900
GeneDependencyModel-class  5.844  0.004   5.853
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/pint.Rcheck/00check.log’
for details.



Installation output

pint.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL pint
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘pint’ ...
** 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 (pint)

Tests output


Example timings

pint.Rcheck/pint-Ex.timings

nameusersystemelapsed
ChromosomeModels-class21.600 0.02021.631
GeneDependencyModel-class5.8440.0045.853
fit.byname0.0520.0000.053
get.neighboring.probes000
get.neighs000
join.top.regions0.0000.0000.001
order.feature.info0.0000.0000.001
pint.data0.0560.0000.054
plot5.8920.0045.900
screen23.588 0.02023.628
summarize.region.parameters0.0000.0000.001
window0.0680.0040.073
z.effect0.0480.0040.052