BioC 2.14: CHECK report for shinyTANDEM on petty

Package: shinyTANDEM

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch shinyTANDEM_1.2.0.tar.gz

StartedAt: 2014-10-08 00:06:49 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:08:18 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 89.8 seconds

RetCode: 0

Status:  OK

CheckDir: shinyTANDEM.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 --no-multiarch shinyTANDEM_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/shinyTANDEM.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘shinyTANDEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘shinyTANDEM’ 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 ‘shinyTANDEM’ can be installed ... [7s/8s] 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 ... NOTE
Packages in Depends field not imported from:
  ‘methods’ ‘mixtools’ ‘rTANDEM’ ‘shiny’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
shinyTandemServer: no visible binding for global variable ‘dataset’
shinyTandemServer: no visible binding for global variable
  ‘expect.value’
shinyTandemServer: no visible binding for global variable
  ‘num.peptides’
shinyTandemServer: no visible binding for global variable ‘prot.uid’
shinyTandemServer: no visible binding for global variable ‘type’
shinyTandemServer: no visible binding for global variable ‘modified’
shinyTandemServer: no visible binding for global variable ‘pep.id’
shinyTandemServer: no visible binding for global variable ‘uid’
shinyTandemServer : <anonymous>: no visible binding for global variable
  ‘pep.id’
shinyTandemServer : <anonymous>: no visible binding for global variable
  ‘at’
shinyTandemServer : <anonymous>: no visible binding for global variable
  ‘type’
shinyTandemServer : <anonymous>: no visible binding for global variable
  ‘modified’
* 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 ... [3s/4s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/shinyTANDEM.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
shinyTANDEM	0.001	0.000	0.000