BioC experimental data: CHECK report for MafDb.ESP6500SI.V2.SSA137.dbSNP138 on perceval

Package: MafDb.ESP6500SI.V2.SSA137.dbSNP138

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.1.0.tar.gz

StartedAt: 2014-04-16 12:17:20 -0700 (Wed, 16 Apr 2014)

EndedAt: 2014-04-16 12:32:19 -0700 (Wed, 16 Apr 2014)

EllapsedTime: 898.9 seconds

RetCode: 0

Status:  OK

CheckDir: MafDb.ESP6500SI.V2.SSA137.dbSNP138.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/MafDb.ESP6500SI.V2.SSA137.dbSNP138.Rcheck’
* using R version 3.1.0 (2014-04-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MafDb.ESP6500SI.V2.SSA137.dbSNP138/DESCRIPTION’ ... OK
* this is package ‘MafDb.ESP6500SI.V2.SSA137.dbSNP138’ version ‘1.1.0’
* 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 ... NOTE
Found the following non-portable file path:
  MafDb.ESP6500SI.V2.SSA137.dbSNP138/inst/MafDbPkgTemplate/man/MafDb.ESP6500SI.V2.SSA137.dbSNP138-package.Rd

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MafDb.ESP6500SI.V2.SSA137.dbSNP138’ can be installed ... [47s/49s] OK
* checking installed package size ... NOTE
  installed size is 76.9Mb
  sub-directories of 1Mb or more:
    extdata  76.8Mb
* checking package 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 ... NOTE
Missing object imported by a ':::' call: ‘VariantFiltering:::dbEasyQuery’
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 examples ... [33s/34s] OK
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/MafDb.ESP6500SI.V2.SSA137.dbSNP138.Rcheck/00check.log’
for details.

* installing *source* package ‘MafDb.ESP6500SI.V2.SSA137.dbSNP138’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (MafDb.ESP6500SI.V2.SSA137.dbSNP138)

name	user	system	elapsed
MafDb.ESP6500SI.V2.SSA137.dbSNP138-package	0.008	0.001	0.009
makeMafDbPackage	0.001	0.001	0.001