BioC 3.2: CHECK report for IMPCdata on oaxaca

Package: IMPCdata

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IMPCdata_1.4.0.tar.gz

StartedAt: 2016-04-23 01:19:53 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:23:27 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 213.2 seconds

RetCode: 0

Status:  OK

CheckDir: IMPCdata.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IMPCdata_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/IMPCdata.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.4.0’
* 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 ‘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 ... [2s/200s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
printAlleles     0.143  0.034  31.496
printGenes       0.135  0.033  31.000
getAlleles       0.133  0.034  37.378
getGenes         0.123  0.032  34.605
getParameters    0.038  0.009   8.591
printParameters  0.036  0.009   8.855
printProcedures  0.035  0.009   8.652
getProcedures    0.033  0.008   8.748
printPhenCenters 0.020  0.007   9.488
getPhenCenters   0.010  0.004   5.232
* 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	0.133	0.034	37.378
getGenes	0.123	0.032	34.605
getIMPCDataset	0.422	0.013	4.013
getIMPCTable	0.008	0.002	2.148
getName	0.001	0.001	0.746
getParameters	0.038	0.009	8.591
getPhenCenters	0.010	0.004	5.232
getPipelines	0.004	0.002	1.779
getProcedures	0.033	0.008	8.748
getStrains	0.007	0.002	2.111
getZygosities	0.002	0.001	0.309
printAlleles	0.143	0.034	31.496
printGenes	0.135	0.033	31.000
printParameters	0.036	0.009	8.855
printPhenCenters	0.020	0.007	9.488
printPipelines	0.004	0.001	1.411
printProcedures	0.035	0.009	8.652
printStrains	0.006	0.001	2.397