BioC 3.5: CHECK report for IMPCdata on oaxaca

Package: IMPCdata

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IMPCdata_1.9.0.tar.gz

StartedAt: 2017-03-04 04:32:40 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 04:46:50 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 850.0 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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/IMPCdata.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.9.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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       0.582  0.188 184.977
printAlleles     0.548  0.177 185.355
printGenes       0.534  0.168 178.207
getGenes         0.527  0.174 179.389
getProcedures    0.040  0.011  10.668
printPhenCenters 0.039  0.006   9.787
printProcedures  0.029  0.008  10.318
getParameters    0.028  0.008   8.618
getPhenCenters   0.025  0.005   5.279
printParameters  0.022  0.007   8.404
* 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	0.582	0.188	184.977
getGenes	0.527	0.174	179.389
getIMPCDataset	0.442	0.015	2.870
getIMPCTable	0.007	0.001	1.489
getName	0.001	0.000	0.385
getParameters	0.028	0.008	8.618
getPhenCenters	0.025	0.005	5.279
getPipelines	0.013	0.003	1.774
getProcedures	0.040	0.011	10.668
getStrains	0.013	0.002	2.429
getZygosities	0.007	0.001	0.309
printAlleles	0.548	0.177	185.355
printGenes	0.534	0.168	178.207
printParameters	0.022	0.007	8.404
printPhenCenters	0.039	0.006	9.787
printPipelines	0.005	0.002	1.882
printProcedures	0.029	0.008	10.318
printStrains	0.006	0.002	2.397