BioC 3.2: CHECK report for ensemblVEP on oaxaca

Package: ensemblVEP

Version: 1.10.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ensemblVEP_1.10.3.tar.gz

StartedAt: 2016-04-22 23:53:03 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-23 00:01:30 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 506.4 seconds

RetCode: 0

Status:  OK

CheckDir: ensemblVEP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ensemblVEP_1.10.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ensemblVEP.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ensemblVEP/DESCRIPTION’ ... OK
* this is package ‘ensemblVEP’ version ‘1.10.3’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ensemblVEP’ can be installed ... [22s/36s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
parseCSQToGRanges,VCF : .local: no visible global function definition
  for ‘elementLengths’
parseCSQToGRanges,VCF : .local: no visible global function definition
  for ‘DataFrame’
parseCSQToGRanges,VCF : .local: no visible global function definition
  for ‘genome<-’
show,VEPParam: no visible global function definition for
  ‘elementLengths’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/144s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ensemblVEP        2.006  0.176  78.619
parseCSQToGRanges 1.894  0.159  53.231
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [17s/123s]
 [17s/123s] 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/ensemblVEP.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
VEPParam-class	0.035	0.001	0.037
ensemblVEP	2.006	0.176	78.619
parseCSQToGRanges	1.894	0.159	53.231
runtimeOptions	0.001	0.001	0.000