Package: curatedBreastData

Version: 2.12.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:curatedBreastData.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings curatedBreastData_2.12.0.tar.gz

StartedAt: 2019-10-17 13:01:42 -0400 (Thu, 17 Oct 2019)

EndedAt: 2019-10-17 13:07:15 -0400 (Thu, 17 Oct 2019)

EllapsedTime: 332.8 seconds

RetCode: 0

Status:  OK

CheckDir: curatedBreastData.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:curatedBreastData.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings curatedBreastData_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/curatedBreastData.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.12.0’
* 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 282.8Mb
  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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
collapseDupProbes            55.781  0.527  56.308
processExpressionSet         33.813  0.208  34.067
filterAndImputeSamples       30.799  0.659  31.459
filterGenesByVariance        28.386  0.165  28.549
removeDuplicatedPatients     28.077  0.136  28.213
curatedBreastDataExprSetList 27.582  0.297  27.879
* 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-3.9-data-experiment/meat/curatedBreastData.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL curatedBreastData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘curatedBreastData’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (curatedBreastData)

name	user	system	elapsed
clinicalData	0.043	0.004	0.046
collapseDupProbes	55.781	0.527	56.308
curatedBreastData-package	0	0	0
curatedBreastDataExprSetList	27.582	0.297	27.879
filterAndImputeSamples	30.799	0.659	31.459
filterGenesByVariance	28.386	0.165	28.549
processExpressionSet	33.813	0.208	34.067
processExpressionSetList	0.000	0.000	0.001
removeDuplicatedPatients	28.077	0.136	28.213