BioC 3.4: CHECK report for annotatr on malbec1

Package: annotatr

Version: 1.0.3

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings annotatr_1.0.3.tar.gz

StartedAt: 2017-04-12 20:55:25 -0400 (Wed, 12 Apr 2017)

EndedAt: 2017-04-12 21:02:05 -0400 (Wed, 12 Apr 2017)

EllapsedTime: 399.5 seconds

RetCode: 0

Status:  OK

CheckDir: annotatr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings annotatr_1.0.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/annotatr.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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           14.628  0.080  15.960
build_annotations            11.000  0.120  12.397
plot_numerical_coannotations 10.564  0.096  11.871
summarize_numerical           5.304  0.068   6.433
summarize_categorical         5.260  0.068   6.576
plot_categorical              5.140  0.104   9.898
annotate_regions              4.648  0.228   8.099
plot_numerical                3.692  0.100   5.594
plot_annotation               3.228  0.104   6.351
summarize_annotations         2.536  0.088   5.084
* 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
  ‘/home/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	4.648	0.228	8.099
annotatr_cache	0.216	0.004	0.218
build_annotations	11.000	0.120	12.397
plot_annotation	3.228	0.104	6.351
plot_categorical	5.140	0.104	9.898
plot_coannotations	14.628	0.080	15.960
plot_numerical	3.692	0.100	5.594
plot_numerical_coannotations	10.564	0.096	11.871
randomize_regions	1.100	0.012	2.090
read_annotations	0.232	0.004	0.237
read_regions	0.860	0.000	0.862
summarize_annotations	2.536	0.088	5.084
summarize_categorical	5.260	0.068	6.576
summarize_numerical	5.304	0.068	6.433
supported_annotations	0.008	0.000	0.006
supported_genomes	0.000	0.000	0.001