Package: Organism.dplyr

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Organism.dplyr_1.6.2.tar.gz

StartedAt: 2018-04-12 07:19:26 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:25:50 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 384.0 seconds

RetCode: 0

Status:  OK

CheckDir: Organism.dplyr.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 Organism.dplyr_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Organism.dplyr.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Organism.dplyr/DESCRIPTION’ ... OK
* this is package ‘Organism.dplyr’ version ‘1.6.2’
* package encoding: UTF-8
* 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 ‘Organism.dplyr’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::smartKeys’ ‘GenomicFeatures:::.exons_with_3utr’
  ‘GenomicFeatures:::.exons_with_5utr’
  ‘GenomicFeatures:::get_TxDb_seqinfo0’
  ‘S4Vectors:::extract_data_frame_rows’
  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
.toGRanges: no visible binding for global variable ‘.’
intronsByTranscript,src_organism: no visible binding for global
  variable ‘.’
orgPackageName,src_organism: no visible binding for global variable
  ‘name’
orgPackageName,src_organism: no visible binding for global variable
  ‘organism’
orgPackageName,src_organism: no visible binding for global variable
  ‘OrgDb’
Undefined global functions or variables:
  . OrgDb name organism
* 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
Genomic-Extractors 6.369  0.083   6.578
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/Organism.dplyr.Rcheck/00check.log’
for details.

* installing *source* package ‘Organism.dplyr’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Organism.dplyr)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> library(testthat)
> library(Organism.dplyr)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: AnnotationFilter

Attaching package: 'AnnotationFilter'

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

    not

> 
> test_check("Organism.dplyr")
Error in result_create(conn@ptr, statement) : database table is locked
Calls: <Anonymous> ... new -> initialize -> initialize -> result_create -> .Call
Error in result_create(conn@ptr, statement) : database table is locked
Calls: <Anonymous> ... new -> initialize -> initialize -> result_create -> .Call
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 201 SKIPPED: 0 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
113.998   3.584 141.242 

name	user	system	elapsed
Genomic-Extractors	6.369	0.083	6.578
filter	0.487	0.004	0.510
select	2.395	0.028	2.477
src	0.296	0.004	0.305
utils	0.003	0.000	0.002