BioC experimental data: CHECK report for curatedBreastData on linux1.bioconductor.org

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: 2015-10-24 14:40:35 -0400 (Sat, 24 Oct 2015)

EndedAt: 2015-10-24 14:46:28 -0400 (Sat, 24 Oct 2015)

EllapsedTime: 352.4 seconds

RetCode: 0

Status:  OK

CheckDir: curatedBreastData.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-data-experiment/meat/curatedBreastData.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ... [4s/4s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [264s/265s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
collapseDupProbes            76.549  0.547  77.173
filterAndImputeSamples       41.165  0.368  41.565
processExpressionSet         38.976  0.116  39.106
filterGenesByVariance        35.928  0.160  36.118
removeDuplicatedPatients     35.003  0.104  35.131
curatedBreastDataExprSetList 34.021  0.212  34.276
* 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	0.049	0.000	0.049
collapseDupProbes	76.549	0.547	77.173
curatedBreastData-package	0.001	0.000	0.001
curatedBreastDataExprSetList	34.021	0.212	34.276
filterAndImputeSamples	41.165	0.368	41.565
filterGenesByVariance	35.928	0.160	36.118
processExpressionSet	38.976	0.116	39.106
processExpressionSetList	0.000	0.004	0.000
removeDuplicatedPatients	35.003	0.104	35.131