BioC 2.13: CHECK report for ensemblVEP on moscato1

Package: ensemblVEP

Version: 1.2.2

Command: rm -rf ensemblVEP.buildbin-libdir && mkdir ensemblVEP.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ensemblVEP.buildbin-libdir ensemblVEP_1.2.2.tar.gz >ensemblVEP-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=ensemblVEP.buildbin-libdir --install="check:ensemblVEP-install.out" --force-multiarch --no-vignettes --timings ensemblVEP_1.2.2.tar.gz && mv ensemblVEP.buildbin-libdir/* ensemblVEP.Rcheck/ && rmdir ensemblVEP.buildbin-libdir

StartedAt: 2014-04-05 03:40:33 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:52:04 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 691.3 seconds

RetCode: 0

Status:  OK

CheckDir: ensemblVEP.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/ensemblVEP.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ensemblVEP/DESCRIPTION' ... OK
* this is package 'ensemblVEP' version '1.2.2'
* 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 whether package 'ensemblVEP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... NOTE
File 'ensemblVEP/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(msg)

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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'ensemblVEP.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [123s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ensemblVEP        1.62   0.05   74.18
parseCSQToGRanges 0.96   0.01   35.60
** running examples for arch 'x64' ... [123s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ensemblVEP        1.98   0.02   71.27
parseCSQToGRanges 1.00   0.03   35.54
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [65s]
 [65s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [66s]
 [68s] 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 were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/ensemblVEP.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'ensemblVEP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ensemblVEP' as ensemblVEP_1.2.2.zip
* DONE (ensemblVEP)

name	user	system	elapsed
VEPParam-class	0.06	0.02	0.08
ensemblVEP	1.62	0.05	74.18
parseCSQToGRanges	0.96	0.01	35.60

name	user	system	elapsed
VEPParam-class	0.09	0.00	0.10
ensemblVEP	1.98	0.02	71.27
parseCSQToGRanges	1.00	0.03	35.54