BioC 3.5: CHECK report for ideal on toluca2

Package: ideal

Version: 0.99.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ideal_0.99.4.tar.gz

StartedAt: 2017-04-23 05:23:41 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:32:27 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 525.7 seconds

RetCode: 0

Status:  OK

CheckDir: ideal.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 ideal_0.99.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ideal.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ideal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ideal’ version ‘0.99.4’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ideal’ 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
ideal: no visible binding for '<<-' assignment to ‘ideal_env’
ideal : <anonymous>: no visible binding for global variable ‘airway’
ideal : <anonymous>: no visible binding for global variable ‘ideal_env’
Undefined global functions or variables:
  airway ideal_env
* 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_ma      43.181  1.282  44.536
plot_volcano 38.563  0.740  39.403
goseqTable   38.478  0.613  39.138
ggplotCounts  6.800  0.145   6.955
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ideal.Rcheck/00check.log’
for details.

* installing *source* package ‘ideal’ ...
** R
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (ideal)

name	user	system	elapsed
deseqresult2DEgenes	2.461	0.019	2.484
deseqresult2tbl	3.119	0.013	3.137
ggplotCounts	6.800	0.145	6.955
goseqTable	38.478	0.613	39.138
ideal	2.007	0.073	2.083
plot_ma	43.181	1.282	44.536
plot_volcano	38.563	0.740	39.403
sepguesser	0.009	0.000	0.010