BioC experimental data: CHECK report for curatedBreastData on zin2

Package: curatedBreastData

Version: 1.4.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_1.4.0.tar.gz

StartedAt: 2016-10-08 09:18:10 -0700 (Sat, 08 Oct 2016)

EndedAt: 2016-10-08 09:23:41 -0700 (Sat, 08 Oct 2016)

EllapsedTime: 331.7 seconds

RetCode: 0

Status:  OK

CheckDir: curatedBreastData.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.4.0’
* 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            76.298  0.923  77.264
processExpressionSet         37.398  0.436  37.856
filterAndImputeSamples       36.770  0.552  37.354
filterGenesByVariance        32.444  0.156  32.582
curatedBreastDataExprSetList 32.067  0.176  32.247
removeDuplicatedPatients     31.896  0.288  32.225
* 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-3.3-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	0.063	0.004	0.166
collapseDupProbes	76.298	0.923	77.264
curatedBreastData-package	0.001	0.000	0.001
curatedBreastDataExprSetList	32.067	0.176	32.247
filterAndImputeSamples	36.770	0.552	37.354
filterGenesByVariance	32.444	0.156	32.582
processExpressionSet	37.398	0.436	37.856
processExpressionSetList	0.001	0.000	0.000
removeDuplicatedPatients	31.896	0.288	32.225