Package: shinyTANDEM

Version: 1.21.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:shinyTANDEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings shinyTANDEM_1.21.1.tar.gz

StartedAt: 2019-04-09 05:55:06 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:56:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 70.4 seconds

RetCode: 0

Status:  OK

CheckDir: shinyTANDEM.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:shinyTANDEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings shinyTANDEM_1.21.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/shinyTANDEM.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'shinyTANDEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'shinyTANDEM' version '1.21.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/shinyTANDEM.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/shinyTANDEM_1.21.1.tar.gz && rm -rf shinyTANDEM.buildbin-libdir && mkdir shinyTANDEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=shinyTANDEM.buildbin-libdir shinyTANDEM_1.21.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL shinyTANDEM_1.21.1.zip && rm shinyTANDEM_1.21.1.tar.gz shinyTANDEM_1.21.1.zip
###
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install for i386

* installing *source* package 'shinyTANDEM' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'shinyTANDEM'
    finding HTML links ... done
    shinyTANDEM                             html  
** building package indices
** installing vignettes
   'shinyTANDEM.Rnw' 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'shinyTANDEM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'shinyTANDEM' as shinyTANDEM_1.21.1.zip
* DONE (shinyTANDEM)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'shinyTANDEM' successfully unpacked and MD5 sums checked