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CHECK report for shinyTANDEM on merida1

This page was generated on 2019-04-16 11:57:13 -0400 (Tue, 16 Apr 2019).

Package 1434/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
shinyTANDEM 1.20.1
Frederic Fournier
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/shinyTANDEM
Branch: RELEASE_3_8
Last Commit: e6558f0
Last Changed Date: 2019-01-04 13:50:13 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: shinyTANDEM
Version: 1.20.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:shinyTANDEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings shinyTANDEM_1.20.1.tar.gz
StartedAt: 2019-04-16 02:46:37 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:47:31 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 53.8 seconds
RetCode: 0
Status:  OK 
CheckDir: shinyTANDEM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:shinyTANDEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings shinyTANDEM_1.20.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/shinyTANDEM.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.20.1’
* 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 ... 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 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Progress: no visible global function definition for ‘new’
analysis.ui: no visible global function definition for ‘div’
analysis.ui: no visible global function definition for ‘h2’
analysis.ui: no visible global function definition for ‘p’
biomart.ui: no visible global function definition for ‘div’
biomart.ui: no visible global function definition for ‘h2’
biomart.ui: no visible global function definition for ‘p’
convert.ui: no visible global function definition for ‘div’
convert.ui: no visible global function definition for ‘h2’
convert.ui: no visible global function definition for ‘p’
external.ui: no visible global function definition for ‘h3’
gominer.ui: no visible global function definition for ‘div’
gominer.ui: no visible global function definition for ‘h2’
gominer.ui: no visible global function definition for ‘p’
home.ui: no visible global function definition for ‘div’
home.ui: no visible binding for global variable ‘tags’
launch.ui: no visible global function definition for ‘div’
launch.ui: no visible global function definition for ‘h2’
launch.ui: no visible global function definition for ‘p’
load.ui: no visible global function definition for ‘div’
load.ui: no visible global function definition for ‘h4’
load.ui: no visible global function definition for ‘h5’
load.ui: no visible global function definition for ‘tag’
load.ui: no visible global function definition for ‘span’
load.ui: no visible binding for global variable ‘tags’
load.ui: no visible global function definition for ‘actionButton’
load.ui: no visible global function definition for ‘uiOutput’
navSection: no visible global function definition for ‘tagList’
navSection: no visible global function definition for ‘singleton’
navSection: no visible binding for global variable ‘tags’
navSection: no visible global function definition for ‘includeHTML’
overview.ui: no visible global function definition for ‘div’
overview.ui: no visible global function definition for ‘h3’
overview.ui: no visible global function definition for ‘htmlOutput’
param.ui: no visible global function definition for ‘div’
param.ui: no visible global function definition for ‘h2’
param.ui: no visible global function definition for ‘p’
peps.ui: no visible global function definition for ‘div’
peps.ui: no visible global function definition for ‘h3’
peps.ui: no visible global function definition for ‘textInput’
peps.ui: no visible global function definition for ‘uiOutput’
peps.ui: no visible binding for global variable ‘tags’
peps.ui: no visible global function definition for ‘htmlOutput’
progressInit: no visible global function definition for ‘tagList’
progressInit: no visible global function definition for ‘singleton’
progressInit: no visible binding for global variable ‘tags’
prots.ui: no visible global function definition for ‘div’
prots.ui: no visible global function definition for ‘h3’
prots.ui: no visible global function definition for ‘numericInput’
prots.ui: no visible global function definition for ‘textInput’
prots.ui: no visible global function definition for ‘uiOutput’
prots.ui: no visible binding for global variable ‘tags’
prots.ui: no visible global function definition for ‘htmlOutput’
shinyTANDEM: no visible global function definition for
  ‘addResourcePath’
shinyTANDEM: no visible global function definition for ‘is’
shinyTANDEM: no visible global function definition for ‘runApp’
shinyTandemServer: no visible global function definition for
  ‘reactiveValues’
shinyTandemServer: no visible global function definition for ‘reactive’
shinyTandemServer: no visible global function definition for ‘isolate’
shinyTandemServer: no visible global function definition for ‘is’
shinyTandemServer: no visible global function definition for
  ‘GetResultsFromXML’
shinyTandemServer: no visible binding for global variable ‘dataset’
shinyTandemServer: no visible global function definition for ‘observe’
shinyTandemServer: no visible global function definition for ‘renderUI’
shinyTandemServer: no visible global function definition for ‘div’
shinyTandemServer: no visible global function definition for
  ‘renderText’
shinyTandemServer: no visible binding for global variable
  ‘expect.value’
shinyTandemServer: no visible binding for global variable
  ‘num.peptides’
shinyTandemServer: no visible global function definition for ‘like’
shinyTandemServer: no visible binding for global variable ‘label’
shinyTandemServer: no visible global function definition for
  ‘selectInput’
shinyTandemServer: no visible binding for global variable ‘prot.uid’
shinyTandemServer: no visible global function definition for ‘HTML’
shinyTandemServer: no visible global function definition for
  ‘tabsetPanel’
shinyTandemServer: no visible global function definition for ‘tabPanel’
shinyTandemServer: no visible global function definition for
  ‘plotOutput’
shinyTandemServer: no visible global function definition for ‘helpText’
shinyTandemServer: no visible global function definition for
  ‘renderPlot’
shinyTandemServer: no visible global function definition for ‘plot’
shinyTandemServer: no visible global function definition for ‘points’
shinyTandemServer: no visible global function definition for ‘abline’
shinyTandemServer: no visible global function definition for ‘legend’
shinyTandemServer: no visible binding for global variable ‘tabsetPanel’
shinyTandemServer : plotChargeDis: no visible global function
  definition for ‘plot’
shinyTandemServer : plotChargeDis: no visible global function
  definition for ‘normalmixEM’
shinyTandemServer : plotChargeDis: no visible global function
  definition for ‘lines’
shinyTandemServer : plotChargeDis: no visible global function
  definition for ‘density’
shinyTandemServer : plotChargeDis: no visible global function
  definition for ‘legend’
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’
shinyTandemServer : <anonymous>: no visible global function definition
  for ‘tabPanel’
shinyTandemServer : <anonymous>: no visible global function definition
  for ‘plotOutput’
shinyUI: no visible global function definition for ‘basicPage’
shinyUI: no visible global function definition for ‘conditionalPanel’
stats.ui: no visible global function definition for ‘div’
stats.ui: no visible global function definition for ‘h3’
stats.ui: no visible global function definition for ‘uiOutput’
tableAsHTML: no visible global function definition for ‘capture.output’
tableAsHTML: no visible global function definition for ‘xtable’
Undefined global functions or variables:
  GetResultsFromXML HTML abline actionButton addResourcePath at
  basicPage capture.output conditionalPanel dataset density div
  expect.value h2 h3 h4 h5 helpText htmlOutput includeHTML is isolate
  label legend like lines modified new normalmixEM num.peptides
  numericInput observe p pep.id plot plotOutput points prot.uid
  reactive reactiveValues renderPlot renderText renderUI runApp
  selectInput singleton span tabPanel tabsetPanel tag tagList tags
  textInput type uiOutput uid xtable
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "density")
  importFrom("utils", "capture.output")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... 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-3.8-bioc/meat/shinyTANDEM.Rcheck/00check.log’
for details.



Installation output

shinyTANDEM.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL shinyTANDEM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘shinyTANDEM’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘shinyTANDEM.Rnw’ 
** testing if installed package can be loaded
* DONE (shinyTANDEM)

Tests output


Example timings

shinyTANDEM.Rcheck/shinyTANDEM-Ex.timings

nameusersystemelapsed
shinyTANDEM000