BioC 3.2: CHECK report for shinyMethyl on oaxaca

Package: shinyMethyl

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings shinyMethyl_1.4.0.tar.gz

StartedAt: 2015-10-27 07:54:07 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:59:58 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 351.4 seconds

RetCode: 0

Status:  OK

CheckDir: shinyMethyl.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 shinyMethyl_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/shinyMethyl.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘shinyMethyl/DESCRIPTION’ ... OK
* this is package ‘shinyMethyl’ version ‘1.4.0’
* 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 ... 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 ‘shinyMethyl’ can be installed ... [22s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘mouse.click.indices’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘colorSet’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘genderCutoff’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘current.control.type’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘current.probe.type’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
  assignment to ‘current.density.type’
server.shinyMethyl : <anonymous>: no visible binding for global
  variable ‘current.control.type’
server.shinyMethyl : <anonymous>: no visible binding for global
  variable ‘mouse.click.indices’
server.shinyMethyl : <anonymous>: no visible binding for global
  variable ‘current.probe.type’
server.shinyMethyl : <anonymous>: no visible binding for global
  variable ‘current.density.type’
server.shinyMethyl : <anonymous>: no visible binding for global
  variable ‘genderCutoff’
ui.shinyMethyl: no visible binding for '<<-' assignment to
  ‘sampleColors’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [63s/64s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
shinySummarize-methods 48.077  3.215   52.69
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [53s/53s]
 [53s/53s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/shinyMethyl.Rcheck/00check.log’
for details.

* installing *source* package ‘shinyMethyl’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
* DONE (shinyMethyl)

name	user	system	elapsed
runShinyMethyl	0	0	0
shinyMethylSet-class	0.001	0.000	0.002
shinySummarize-methods	48.077	3.215	52.690