BioC 3.5: CHECK report for annotatr on oaxaca

Package: annotatr

Version: 1.1.12

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotatr_1.1.12.tar.gz

StartedAt: 2017-03-03 23:06:48 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:18:49 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 720.8 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_1.1.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/annotatr.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.1.12’
* 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           17.906  0.386  21.641
plot_numerical_coannotations 13.318  0.427  16.510
build_annotations            12.199  0.570  16.271
annotate_regions              8.817  0.558  28.679
plot_categorical              7.146  0.510  14.280
summarize_categorical         6.877  0.359  11.013
summarize_numerical           5.764  0.341   9.062
plot_annotation               4.713  0.356  12.319
plot_numerical                4.310  0.363   8.211
summarize_annotations         4.158  0.301  10.355
build_ah_annots               2.238  0.278   8.479
* 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-3.5-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	8.817	0.558	28.679
annotatr_cache	0.378	0.011	0.390
build_ah_annots	2.238	0.278	8.479
build_annotations	12.199	0.570	16.271
builtin_annotations	0.012	0.003	0.014
builtin_genomes	0.001	0.000	0.001
plot_annotation	4.713	0.356	12.319
plot_categorical	7.146	0.510	14.280
plot_coannotations	17.906	0.386	21.641
plot_numerical	4.310	0.363	8.211
plot_numerical_coannotations	13.318	0.427	16.510
randomize_regions	0.968	0.046	4.167
read_annotations	0.284	0.006	0.290
read_regions	0.462	0.010	0.471
summarize_annotations	4.158	0.301	10.355
summarize_categorical	6.877	0.359	11.013
summarize_numerical	5.764	0.341	9.062