BioC 3.4: CHECK report for miRNAtap on malbec1

Package: miRNAtap

Version: 1.8.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings miRNAtap_1.8.0.tar.gz

StartedAt: 2017-04-14 23:54:33 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:56:17 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 103.6 seconds

RetCode: 0

Status:  OK

CheckDir: miRNAtap.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 miRNAtap_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/miRNAtap.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 ‘miRNAtap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRNAtap’ version ‘1.8.0’
* 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 ‘miRNAtap’ 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 ... NOTE
'library' or 'require' call to ‘miRNAtap.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getTargetsFromSource: no visible binding for global variable
  ‘miRNAtap.db’
getTargetsFromSource : <anonymous>: no visible binding for global
  variable ‘miRNAtap.db’
translate: no visible binding for global variable ‘miRNAtap.db’
Undefined global functions or variables:
  miRNAtap.db
* 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
getPredictedTargets 3.664  0.704  22.411
miRNAtap            2.024  0.392  13.454
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/miRNAtap.Rcheck/00check.log’
for details.

* installing *source* package ‘miRNAtap’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (miRNAtap)

name	user	system	elapsed
MirnaDb-class	0.060	0.008	0.465
aggregateRanks	0.008	0.000	0.010
getPredictedTargets	3.664	0.704	22.411
getTargetsFromSource	0.456	0.028	0.483
miRNAtap	2.024	0.392	13.454
translate	0.056	0.004	0.058