BioC experimental data: CHECK report for curatedBreastData on zin1

Package: curatedBreastData

Version: 1.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_1.2.0.tar.gz

StartedAt: 2016-04-20 11:14:29 -0700 (Wed, 20 Apr 2016)

EndedAt: 2016-04-20 11:20:25 -0700 (Wed, 20 Apr 2016)

EllapsedTime: 355.8 seconds

RetCode: 0

Status:  OK

CheckDir: curatedBreastData.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-data-experiment/meat/curatedBreastData.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.2.0’
* 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 ... [3s/5s] 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 ... OK
* 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 ... [267s/270s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
collapseDupProbes            79.823  1.032  81.656
processExpressionSet         40.541  0.284  41.168
filterAndImputeSamples       40.211  0.435  41.632
filterGenesByVariance        34.891  0.185  35.217
curatedBreastDataExprSetList 33.652  0.511  34.930
removeDuplicatedPatients     33.898  0.091  34.400
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-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	0.081	0.000	0.081
collapseDupProbes	79.823	1.032	81.656
curatedBreastData-package	0.002	0.000	0.001
curatedBreastDataExprSetList	33.652	0.511	34.930
filterAndImputeSamples	40.211	0.435	41.632
filterGenesByVariance	34.891	0.185	35.217
processExpressionSet	40.541	0.284	41.168
processExpressionSetList	0.001	0.000	0.000
removeDuplicatedPatients	33.898	0.091	34.400