BioC experimental data: CHECK report for curatedBreastData on zin1

Package: curatedBreastData

Version: 1.5.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_1.5.0.tar.gz

StartedAt: 2016-08-20 11:29:13 -0700 (Sat, 20 Aug 2016)

EndedAt: 2016-08-20 11:34:53 -0700 (Sat, 20 Aug 2016)

EllapsedTime: 339.6 seconds

RetCode: 0

Status:  OK

CheckDir: curatedBreastData.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/curatedBreastData.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘curatedBreastData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedBreastData’ version ‘1.5.0’
* 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 ‘curatedBreastData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 283.0Mb
  sub-directories of 1Mb or more:
    data  282.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
collapseDupProbes: no visible global function definition for ‘cov’
filterAndImputeSamples: no visible global function definition for
  ‘na.omit’
filterGenesByVariance : <anonymous>: no visible global function
  definition for ‘var’
filterGenesByVariance: no visible global function definition for
  ‘median’
filterGenesByVariance: no visible global function definition for
  ‘quantile’
processExpressionSet: no visible global function definition for
  ‘validObject’
processExpressionSet: no visible global function definition for
  ‘na.omit’
removeDuplicatedPatients : <anonymous>: no visible global function
  definition for ‘var’
Undefined global functions or variables:
  cov median na.omit quantile validObject var
Consider adding
  importFrom("methods", "validObject")
  importFrom("stats", "cov", "median", "na.omit", "quantile", "var")
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
collapseDupProbes            75.656  3.444  79.587
filterAndImputeSamples       35.624  1.712  37.351
processExpressionSet         36.032  0.500  36.564
filterGenesByVariance        31.484  0.560  32.046
curatedBreastDataExprSetList 30.676  1.152  31.866
removeDuplicatedPatients     30.844  0.288  31.136
* 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-3.4-data-experiment/meat/curatedBreastData.Rcheck/00check.log’
for details.

* installing *source* package ‘curatedBreastData’ ...
** 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 (curatedBreastData)

name	user	system	elapsed
clinicalData	0.060	0.016	0.077
collapseDupProbes	75.656	3.444	79.587
curatedBreastData-package	0.000	0.000	0.001
curatedBreastDataExprSetList	30.676	1.152	31.866
filterAndImputeSamples	35.624	1.712	37.351
filterGenesByVariance	31.484	0.560	32.046
processExpressionSet	36.032	0.500	36.564
processExpressionSetList	0.000	0.000	0.001
removeDuplicatedPatients	30.844	0.288	31.136