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BioC 3.4: CHECK report for pint on moscato1

This page was generated on 2016-09-21 03:42:57 -0700 (Wed, 21 Sep 2016).

Package 901/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pint 1.23.0
Olli-Pekka Huovilainen
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pint
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pint
Version: 1.23.0
Command: rm -rf pint.buildbin-libdir pint.Rcheck && mkdir pint.buildbin-libdir pint.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pint.buildbin-libdir pint_1.23.0.tar.gz >pint.Rcheck\00install.out 2>&1 && cp pint.Rcheck\00install.out pint-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=pint.buildbin-libdir --install="check:pint-install.out" --force-multiarch --no-vignettes --timings pint_1.23.0.tar.gz
StartedAt: 2016-09-20 13:59:58 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 14:04:39 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 280.2 seconds
RetCode: 0
Status:  OK  
CheckDir: pint.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf pint.buildbin-libdir pint.Rcheck && mkdir pint.buildbin-libdir pint.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pint.buildbin-libdir pint_1.23.0.tar.gz >pint.Rcheck\00install.out 2>&1 && cp pint.Rcheck\00install.out pint-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=pint.buildbin-libdir --install="check:pint-install.out" --force-multiarch --no-vignettes --timings pint_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/pint.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pint/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pint' version '1.23.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
screen                    39.17   0.02   39.19
ChromosomeModels-class    34.50   0.03   34.58
plot                       9.79   0.01    9.80
GeneDependencyModel-class  9.32   0.00    9.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
screen                    48.07   0.05   48.11
ChromosomeModels-class    43.18   0.02   43.26
plot                      11.57   0.00   11.58
GeneDependencyModel-class 11.45   0.00   11.56
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/pint.Rcheck/00check.log'
for details.


pint.Rcheck/00install.out:


install for i386

* installing *source* package 'pint' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'as.data.frame' from package 'base' in package 'pint'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'pint' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pint' as pint_1.23.0.zip
* DONE (pint)

pint.Rcheck/examples_i386/pint-Ex.timings:

nameusersystemelapsed
ChromosomeModels-class34.50 0.0334.58
GeneDependencyModel-class9.320.009.33
fit.byname0.100.000.09
get.neighboring.probes000
get.neighs000
join.top.regions000
order.feature.info000
pint.data0.140.020.16
plot9.790.019.80
screen39.17 0.0239.19
summarize.region.parameters000
window0.110.020.12
z.effect0.060.000.07

pint.Rcheck/examples_x64/pint-Ex.timings:

nameusersystemelapsed
ChromosomeModels-class43.18 0.0243.26
GeneDependencyModel-class11.45 0.0011.56
fit.byname0.110.000.11
get.neighboring.probes000
get.neighs000
join.top.regions000
order.feature.info000
pint.data0.160.010.17
plot11.57 0.0011.58
screen48.07 0.0548.11
summarize.region.parameters000
window0.150.000.15
z.effect0.10.00.1