BioC 3.6: CHECK report for annotatr on veracruz1

Package: annotatr

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotatr_1.3.2.tar.gz

StartedAt: 2017-08-15 23:56:01 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-16 00:01:50 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 348.8 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 --no-vignettes --timings annotatr_1.3.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/annotatr.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.3.2’
* 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 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
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
build_annotations 5.113  0.159   5.401
* 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-3.6-bioc/meat/annotatr.Rcheck/00check.log’
for details.

* installing *source* package ‘annotatr’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (annotatr)

name	user	system	elapsed
annotate_regions	1.006	0.012	1.036
annotatr_cache	1.269	0.073	1.376
build_ah_annots	3.141	0.172	4.467
build_annotations	5.113	0.159	5.401
builtin_annotations	0.011	0.002	0.014
builtin_genomes	0.000	0.001	0.001
plot_annotation	2.208	0.084	3.272
plot_categorical	1.915	0.054	3.009
plot_coannotations	2.418	0.042	2.515
plot_numerical	0.550	0.014	0.573
plot_numerical_coannotations	0.985	0.032	1.033
randomize_regions	0.943	0.021	1.976
read_annotations	0.372	0.013	0.388
read_regions	0.479	0.020	0.507
summarize_annotations	1.351	0.056	3.584
summarize_categorical	0.436	0.030	0.475
summarize_numerical	0.487	0.020	0.512