BioC experimental data: CHECK report for curatedBreastData on malbec2

Package: curatedBreastData

Version: 2.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_2.4.0.tar.gz

StartedAt: 2017-10-18 10:38:14 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 10:43:27 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 312.3 seconds

RetCode: 0

Status:  OK

CheckDir: curatedBreastData.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings curatedBreastData_2.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/curatedBreastData.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘2.4.0’
* 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 283.1Mb
  sub-directories of 1Mb or more:
    data  282.7Mb
* 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 ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
collapseDupProbes            66.148  1.204  67.396
filterAndImputeSamples       34.228  2.076  36.321
processExpressionSet         35.676  0.496  36.196
filterGenesByVariance        31.268  0.420  31.711
removeDuplicatedPatients     30.664  0.480  31.162
curatedBreastDataExprSetList 30.456  0.544  31.017
* 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-3.5-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	0.056	0.004	0.060
collapseDupProbes	66.148	1.204	67.396
curatedBreastData-package	0.000	0.000	0.001
curatedBreastDataExprSetList	30.456	0.544	31.017
filterAndImputeSamples	34.228	2.076	36.321
filterGenesByVariance	31.268	0.420	31.711
processExpressionSet	35.676	0.496	36.196
processExpressionSetList	0.000	0.000	0.001
removeDuplicatedPatients	30.664	0.480	31.162