Package: annotatr

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annotatr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotatr_1.9.0.tar.gz

StartedAt: 2019-04-08 23:14:52 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:20:50 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 357.8 seconds

RetCode: 0

Status:  OK

CheckDir: annotatr.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annotatr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotatr_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/annotatr.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotatr/DESCRIPTION’ ... OK
* this is package ‘annotatr’ version ‘1.9.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘annotatr’ 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 ... NOTE
plot_coannotations: no visible binding for global variable ‘.’
plot_numerical_coannotations: no visible binding for global variable
  ‘.’
Undefined global functions or variables:
  .
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
build_ah_annots   13.420  1.489  23.565
build_annotations  5.178  0.237   5.488
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/annotatr.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL annotatr
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘annotatr’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (annotatr)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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(annotatr)
> 
> test_check("annotatr")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 72 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 44.221   2.665  69.668 

name	user	system	elapsed
annotate_regions	1.064	0.030	1.104
annotatr_cache	1.851	0.272	2.198
build_ah_annots	13.420	1.489	23.565
build_annotations	5.178	0.237	5.488
builtin_annotations	0.009	0.002	0.011
builtin_genomes	0.000	0.001	0.000
plot_annotation	1.923	0.058	2.858
plot_categorical	1.180	0.060	2.114
plot_coannotations	0.860	0.018	0.885
plot_numerical	0.399	0.027	0.428
plot_numerical_coannotations	0.591	0.019	0.619
randomize_regions	0.756	0.018	1.631
read_annotations	0.266	0.008	0.273
read_regions	0.295	0.011	0.307
summarize_annotations	0.978	0.029	1.875
summarize_categorical	0.447	0.017	0.484
summarize_numerical	0.386	0.017	0.404