BioC 2.13: CHECK report for h5vc on perceval

Package: h5vc

Version: 1.0.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch h5vc_1.0.6.tar.gz

StartedAt: 2014-04-05 01:56:12 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:59:44 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 212.0 seconds

RetCode: 0

Status:  OK

CheckDir: h5vc.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/h5vc.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘h5vc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘h5vc’ version ‘1.0.6’
* 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 ‘h5vc’ can be installed ... [17s/17s] 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 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 ... NOTE
File ‘h5vc/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("*NOTE:* h5vc is a package under constant development and many improvements over this version have accumulated in the development branch.\nPlease switch to the development version of h5vc (>=1.1.18) for production use.")

See section ‘Good practice’ in '?.onAttach'.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutationSpectrum 9.272  0.344  10.071
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/h5vc.Rcheck/00check.log’
for details.

* installing *source* package ‘h5vc’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘GenomicRanges::%in%’ when loading ‘h5vc’
Warning: replacing previous import by ‘GenomicRanges::match’ when loading ‘h5vc’
Warning: replacing previous import by ‘GenomicRanges::order’ when loading ‘h5vc’
Warning: replacing previous import by ‘GenomicRanges::rank’ when loading ‘h5vc’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘GenomicRanges::%in%’ when loading ‘h5vc’
Warning: replacing previous import by ‘GenomicRanges::match’ when loading ‘h5vc’
Warning: replacing previous import by ‘GenomicRanges::order’ when loading ‘h5vc’
Warning: replacing previous import by ‘GenomicRanges::rank’ when loading ‘h5vc’
* DONE (h5vc)

name	user	system	elapsed
callVariants	1.769	0.261	2.063
coverage	3.038	0.265	3.339
geom_h5vc	1.456	0.101	1.577
getSampleData	0.086	0.002	0.089
h5dapply	0.396	0.018	0.418
helpers	0.305	0.015	0.324
mismatchPlot	2.571	0.101	2.740
mutationSpectrum	9.272	0.344	10.071