BioC 3.5: CHECK report for Anaquin on veracruz2

Package: Anaquin

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Anaquin_1.2.0.tar.gz

StartedAt: 2017-10-18 00:21:24 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:25:57 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 272.1 seconds

RetCode: 0

Status:  OK

CheckDir: Anaquin.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 Anaquin_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Anaquin.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Anaquin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Anaquin’ version ‘1.2.0’
* 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 ‘Anaquin’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’
A package should be listed in only one of these fields.
* 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
RnaQuin.genes: no visible binding for global variable ‘RnaQuinMixtureA’
RnaQuin.isoforms: no visible binding for global variable
  ‘RnaQuinMixtureA’
Undefined global functions or variables:
  RnaQuinMixtureA
* 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 sizes of PDF files under ‘inst/doc’ ... 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
AnaquinData 6.94  0.079   7.229
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tAnaquin.R’
  Running ‘tPlotLODR.R’
  Running ‘tPlotLinear.R’
  Running ‘tPlotLogistic.R’
  Running ‘tPlotMA.R’
  Running ‘tPlotROC.R’
  Running ‘tRnaQuin.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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Anaquin.Rcheck/00check.log’
for details.

* installing *source* package ‘Anaquin’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for ‘mean’ in package ‘Anaquin’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Anaquin)

name	user	system	elapsed
AnaquinData	6.940	0.079	7.229
RnaQuin.aggregate	0.008	0.001	0.010
RnaQuin.genes	0.002	0.000	0.002
RnaQuin.iso2gen	0.001	0.000	0.001
RnaQuin.isoforms	0.001	0.001	0.003
analysis	0.002	0.000	0.003
input	0.004	0.001	0.005
label	0.004	0.001	0.005
measured	0.008	0.002	0.009
plotLODR	0.545	0.004	0.566
plotLinear	1.591	0.010	1.655
plotLogistic	1.179	0.009	1.213
plotMA	0.341	0.005	0.358
plotROC	0.444	0.004	0.456
pval	0.004	0.001	0.005
qval	0.005	0.001	0.005
ratio	0.004	0.001	0.006
score	0.004	0.001	0.005
seqs	0.004	0.001	0.005
std	0.004	0.001	0.006