BioC experimental data: CHECK report for curatedBreastData on morelia

Package: curatedBreastData

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings curatedBreastData_1.3.0.tar.gz

StartedAt: 2015-11-25 10:18:39 -0800 (Wed, 25 Nov 2015)

EndedAt: 2015-11-25 10:26:59 -0800 (Wed, 25 Nov 2015)

EllapsedTime: 499.7 seconds

RetCode: 0

Status:  OK

CheckDir: curatedBreastData.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings curatedBreastData_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/curatedBreastData.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.0’
* 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 ... [4s/81s] 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 ... [249s/284s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
collapseDupProbes            74.420  1.258  88.780
filterAndImputeSamples       37.198  2.395  45.239
removeDuplicatedPatients     34.627  1.050  40.334
processExpressionSet         33.441  1.668  40.218
curatedBreastDataExprSetList 30.026  0.817  34.129
filterGenesByVariance        29.588  0.795  31.514
* 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
  ‘/Users/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	0.053	0.007	0.753
collapseDupProbes	74.420	1.258	88.780
curatedBreastData-package	0.001	0.000	0.116
curatedBreastDataExprSetList	30.026	0.817	34.129
filterAndImputeSamples	37.198	2.395	45.239
filterGenesByVariance	29.588	0.795	31.514
processExpressionSet	33.441	1.668	40.218
processExpressionSetList	0.001	0.000	0.001
removeDuplicatedPatients	34.627	1.050	40.334