BioC 2.13: CHECK report for h5vc on zin1

Package: h5vc

Version: 1.0.6

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings h5vc_1.0.6.tar.gz

StartedAt: 2014-04-05 01:47:21 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:49:19 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 118.3 seconds

RetCode: 0

Status:  OK

CheckDir: h5vc.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/h5vc.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [10s/10s] 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 ... [16s/16s] OK
* 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
  ‘/home/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	1.224	0.012	1.239
coverage	2.544	0.008	2.559
geom_h5vc	0.964	0.008	0.974
getSampleData	0.068	0.000	0.069
h5dapply	0.440	0.012	0.452
helpers	0.120	0.008	0.131
mismatchPlot	1.388	0.012	1.401
mutationSpectrum	4.416	0.036	4.461