BioC 3.4: CHECK report for annotatr on morelia

Package: annotatr

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotatr_1.0.3.tar.gz

StartedAt: 2017-04-13 22:34:07 -0700 (Thu, 13 Apr 2017)

EndedAt: 2017-04-13 22:42:19 -0700 (Thu, 13 Apr 2017)

EllapsedTime: 491.2 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_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/annotatr.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotatr/DESCRIPTION’ ... OK
* this is package ‘annotatr’ version ‘1.0.3’
* 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 ‘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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
plot_coannotations           14.999  0.329  17.952
build_annotations            12.873  0.523  17.050
plot_numerical_coannotations 11.252  0.319  14.354
plot_categorical              6.822  0.437  13.051
summarize_categorical         6.857  0.312  10.097
summarize_numerical           6.761  0.366   9.713
annotate_regions              6.029  0.494  22.002
plot_numerical                4.814  0.312   8.100
plot_annotation               4.523  0.306  10.755
summarize_annotations         3.981  0.288   9.266
* 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-3.4-bioc/meat/annotatr.Rcheck/00check.log’
for details.

* installing *source* package ‘annotatr’ ...
** R
** 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	6.029	0.494	22.002
annotatr_cache	0.300	0.008	0.309
build_annotations	12.873	0.523	17.050
plot_annotation	4.523	0.306	10.755
plot_categorical	6.822	0.437	13.051
plot_coannotations	14.999	0.329	17.952
plot_numerical	4.814	0.312	8.100
plot_numerical_coannotations	11.252	0.319	14.354
randomize_regions	1.069	0.034	3.592
read_annotations	0.254	0.005	0.260
read_regions	0.864	0.017	0.883
summarize_annotations	3.981	0.288	9.266
summarize_categorical	6.857	0.312	10.097
summarize_numerical	6.761	0.366	9.713
supported_annotations	0.010	0.002	0.012
supported_genomes	0.000	0.000	0.001