BioC 3.5: CHECK report for IMPCdata on veracruz2

Package: IMPCdata

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IMPCdata_1.10.0.tar.gz

StartedAt: 2017-10-18 04:59:48 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:34:38 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 2089.8 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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/IMPCdata.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.0’
* 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       4.408  0.762 486.124
printGenes       4.140  0.693 467.988
getGenes         4.128  0.704 471.923
printAlleles     4.096  0.691 488.228
getProcedures    0.218  0.037  26.267
printProcedures  0.214  0.037  26.456
getParameters    0.197  0.034  21.677
printParameters  0.188  0.031  22.058
printPhenCenters 0.179  0.028  22.218
getPhenCenters   0.099  0.016  11.993
getStrains       0.049  0.008   6.440
printStrains     0.046  0.007   5.515
* 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	4.408	0.762	486.124
getGenes	4.128	0.704	471.923
getIMPCDataset	0.600	0.016	2.814
getIMPCTable	0.033	0.006	3.442
getName	0.008	0.001	1.706
getParameters	0.197	0.034	21.677
getPhenCenters	0.099	0.016	11.993
getPipelines	0.045	0.007	4.301
getProcedures	0.218	0.037	26.267
getStrains	0.049	0.008	6.440
getZygosities	0.014	0.001	0.815
printAlleles	4.096	0.691	488.228
printGenes	4.140	0.693	467.988
printParameters	0.188	0.031	22.058
printPhenCenters	0.179	0.028	22.218
printPipelines	0.038	0.006	4.637
printProcedures	0.214	0.037	26.456
printStrains	0.046	0.007	5.515