BioC 3.6: CHECK report for IMPCdata on malbec1

Package: IMPCdata

Version: 1.11.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings IMPCdata_1.11.0.tar.gz

StartedAt: 2017-08-16 00:03:20 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:16:20 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 780.0 seconds

RetCode: 0

Status:  OK

CheckDir: IMPCdata.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings IMPCdata_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/IMPCdata.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.11.0’
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getAlleles       0.892  0.220 161.628
getGenes         0.860  0.192 156.768
printAlleles     0.908  0.144 160.940
printGenes       0.800  0.192 154.960
printPhenCenters 0.044  0.016   9.683
getProcedures    0.036  0.016   9.302
getParameters    0.048  0.000   7.450
printProcedures  0.032  0.016   9.186
printParameters  0.040  0.004   7.237
getPhenCenters   0.032  0.004   5.278
* 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	0.892	0.220	161.628
getGenes	0.860	0.192	156.768
getIMPCDataset	0.480	0.000	2.612
getIMPCTable	0.008	0.000	1.204
getName	0.004	0.000	0.401
getParameters	0.048	0.000	7.450
getPhenCenters	0.032	0.004	5.278
getPipelines	0.016	0.000	1.604
getProcedures	0.036	0.016	9.302
getStrains	0.012	0.004	1.868
getZygosities	0.008	0.000	0.271
printAlleles	0.908	0.144	160.940
printGenes	0.800	0.192	154.960
printParameters	0.040	0.004	7.237
printPhenCenters	0.044	0.016	9.683
printPipelines	0.004	0.004	1.864
printProcedures	0.032	0.016	9.186
printStrains	0.012	0.000	2.155