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BioC 2.13: CHECK report for h5vc on perceval

This page was generated on 2014-04-05 09:53:18 -0700 (Sat, 05 Apr 2014).

Package 337/750HostnameOS / ArchBUILDCHECKBUILD BIN
h5vc 1.0.6
Paul Theodor Pyl
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/h5vc
Last Changed Rev: 85861 / Revision: 88450
Last Changed Date: 2014-01-28 02:39:29 -0800 (Tue, 28 Jan 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

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

Command output

* 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.

h5vc.Rcheck/00install.out:

* 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)

h5vc.Rcheck/h5vc-Ex.timings:

nameusersystemelapsed
callVariants1.7690.2612.063
coverage3.0380.2653.339
geom_h5vc1.4560.1011.577
getSampleData0.0860.0020.089
h5dapply0.3960.0180.418
helpers0.3050.0150.324
mismatchPlot2.5710.1012.740
mutationSpectrum 9.272 0.34410.071