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BioC 2.14: CHECK report for ensemblVEP on zin2

This page was generated on 2014-10-08 08:49:48 -0700 (Wed, 08 Oct 2014).

Package 256/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ensemblVEP 1.4.4
Valerie Obenchain
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ensemblVEP
Last Changed Rev: 95014 / Revision: 95116
Last Changed Date: 2014-10-06 13:39:54 -0700 (Mon, 06 Oct 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: ensemblVEP
Version: 1.4.4
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ensemblVEP_1.4.4.tar.gz
StartedAt: 2014-10-07 23:24:02 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:31:42 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 460.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ensemblVEP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ensemblVEP_1.4.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/ensemblVEP.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ensemblVEP/DESCRIPTION’ ... OK
* this is package ‘ensemblVEP’ version ‘1.4.4’
* 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 ‘ensemblVEP’ can be installed ... [20s/20s] 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::selectSome’ ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/150s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ensemblVEP        3.580  0.280  93.823
parseCSQToGRanges 1.448  0.116  46.332
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [14s/110s]
 [14s/111s] 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-2.14-bioc/meat/ensemblVEP.Rcheck/00check.log’
for details.

ensemblVEP.Rcheck/00install.out:

* installing *source* package ‘ensemblVEP’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ensemblVEP)

ensemblVEP.Rcheck/ensemblVEP-Ex.timings:

nameusersystemelapsed
VEPParam-class0.0360.0080.047
ensemblVEP 3.580 0.28093.823
parseCSQToGRanges 1.448 0.11646.332
runtimeOptions0.0040.0000.000