BioC 3.2: CHECK report for ensemblVEP on zin1

Package: ensemblVEP

Version: 1.9.3

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ensemblVEP_1.9.3.tar.gz

StartedAt: 2015-08-23 23:34:52 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:44:54 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 602.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ensemblVEP.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ensemblVEP_1.9.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ensemblVEP.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ensemblVEP/DESCRIPTION’ ... OK
* this is package ‘ensemblVEP’ version ‘1.9.3’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ensemblVEP’ can be installed ... [17s/18s] 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 ... WARNING
'::' or ':::' import not declared from: ‘S4Vectors’
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘S4Vectors:::selectSome’
  See the note in ?`:::` about the use of this operator.
* 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 ... [13s/265s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ensemblVEP        2.807  0.325 163.962
parseCSQToGRanges 1.320  0.172  92.566
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/164s]
 [13s/164s] 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: 1 WARNING, 2 NOTEs
See
  ‘/home/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	0.028	0.008	0.036
ensemblVEP	2.807	0.325	163.962
parseCSQToGRanges	1.320	0.172	92.566
runtimeOptions	0	0	0