BioC 3.5: CHECK report for MSGFgui on veracruz2

Package: MSGFgui

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSGFgui_1.10.0.tar.gz

StartedAt: 2017-10-18 06:27:56 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:29:19 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 83.1 seconds

RetCode: 0

Status:  OK

CheckDir: MSGFgui.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 MSGFgui_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MSGFgui.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 ‘MSGFgui/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSGFgui’ version ‘1.10.0’
* 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 ‘MSGFgui’ 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 ... NOTE
Package in Depends field not imported from: ‘xlsx’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getAAtable: no visible global function definition for ‘read.csv’
getAdductTable: no visible global function definition for ‘read.csv’
getIonTrace: no visible global function definition for ‘predict’
getIonTrace: no visible global function definition for ‘loess’
getIonTrace : gauss: no visible global function definition for ‘dnorm’
getIonTrace: no visible global function definition for ‘optimize’
getScoreDistribution: no visible global function definition for
  ‘density’
renderMzID: no visible global function definition for ‘scans’
renderMzID: no visible global function definition for ‘peptides’
renderMzID: no visible global function definition for ‘modifications’
renderMzID: no visible global function definition for ‘database’
server: no visible global function definition for ‘scans’
server : <anonymous>: no visible global function definition for
  ‘createWorkbook’
server : <anonymous>: no visible global function definition for
  ‘createSheet’
server : <anonymous>: no visible global function definition for
  ‘addDataFrame’
server : <anonymous>: no visible global function definition for
  ‘saveWorkbook’
server : <anonymous>: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  addDataFrame createSheet createWorkbook database density dnorm loess
  modifications optimize peptides predict read.csv saveWorkbook scans
  write.table
Consider adding
  importFrom("stats", "density", "dnorm", "loess", "optimize", "predict")
  importFrom("utils", "read.csv", "write.table")
to your NAMESPACE file.
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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/MSGFgui.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
MSGFgui	0.000	0.000	0.001
currentData	0.001	0.000	0.001