Package: ensemblVEP

Version: 1.20.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ensemblVEP_1.20.1.tar.gz

StartedAt: 2018-04-11 23:14:08 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:18:24 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 255.6 seconds

RetCode: 0

Status:  OK

CheckDir: ensemblVEP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ensemblVEP_1.20.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ensemblVEP.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.20.1’
* 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 ... 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 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ensemblVEP        3.432  0.268  17.600
parseCSQToGRanges 1.356  0.180  15.564
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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 NOTE
See
  ‘/home/biocbuild/bbs-3.6-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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("ensemblVEP")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply


Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate


Attaching package: 'ensemblVEP'

The following object is masked from 'package:Biobase':

    cache


-------------------- EXCEPTION --------------------
MSG: ERROR: File "ImNotAFile" does not exist

STACK Bio::EnsEMBL::VEP::Parser::file /usr/local/ensembl-vep-release-92/modules/Bio/EnsEMBL/VEP/Parser.pm:228
STACK Bio::EnsEMBL::VEP::Parser::new /usr/local/ensembl-vep-release-92/modules/Bio/EnsEMBL/VEP/Parser.pm:123
STACK Bio::EnsEMBL::VEP::Runner::get_Parser /usr/local/ensembl-vep-release-92/modules/Bio/EnsEMBL/VEP/Runner.pm:789
STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer /usr/local/ensembl-vep-release-92/modules/Bio/EnsEMBL/VEP/Runner.pm:816
STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/ensembl-vep-release-92/modules/Bio/EnsEMBL/VEP/Runner.pm:131
STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/ensembl-vep-release-92/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel /usr/local/ensembl-vep-release-92/vep:224
Date (localtime)    = Wed Apr 11 23:18:21 2018
Ensembl API version = 92
---------------------------------------------------


RUNIT TEST PROTOCOL -- Wed Apr 11 23:18:21 2018 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ensemblVEP RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 17.452   1.076  34.325 

name	user	system	elapsed
VEPFlags-class	0.012	0.040	0.057
VEPParam-class	0.104	0.048	0.161
ensemblVEP	3.432	0.268	17.600
oldRuntimeOptions	0.004	0.000	0.000
parseCSQToGRanges	1.356	0.180	15.564
runtimeOptions	0.000	0.000	0.001