BioC 3.1: CHECK report for IMPCdata on morelia

Package: IMPCdata

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IMPCdata_1.2.0.tar.gz

StartedAt: 2015-10-09 03:07:10 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:10:28 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 197.4 seconds

RetCode: 0

Status:  OK

CheckDir: IMPCdata.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IMPCdata_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/IMPCdata.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IMPCdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IMPCdata’ 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 ‘IMPCdata’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/183s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getAlleles       0.144  0.033  36.733
printAlleles     0.146  0.031  30.183
getGenes         0.135  0.032  29.547
printGenes       0.137  0.030  29.849
getParameters    0.037  0.008  11.795
printParameters  0.035  0.009   7.710
getProcedures    0.034  0.008   7.444
printProcedures  0.028  0.007   7.404
printPhenCenters 0.020  0.007   8.208
* 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: OK

* installing *source* package ‘IMPCdata’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IMPCdata)

name	user	system	elapsed
getAlleles	0.144	0.033	36.733
getGenes	0.135	0.032	29.547
getIMPCDataset	0.004	0.000	0.356
getIMPCTable	0.008	0.002	1.227
getName	0.001	0.001	0.342
getParameters	0.037	0.008	11.795
getPhenCenters	0.011	0.004	4.124
getPipelines	0.005	0.001	1.643
getProcedures	0.034	0.008	7.444
getStrains	0.008	0.002	1.894
getZygosities	0.002	0.000	0.289
printAlleles	0.146	0.031	30.183
printGenes	0.137	0.030	29.849
printParameters	0.035	0.009	7.710
printPhenCenters	0.020	0.007	8.208
printPipelines	0.004	0.001	1.634
printProcedures	0.028	0.007	7.404
printStrains	0.006	0.002	1.935