BioC 3.2: CHECK report for synapter on oaxaca

Package: synapter

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings synapter_1.12.0.tar.gz

StartedAt: 2016-04-23 04:52:26 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:56:03 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 217.1 seconds

RetCode: 0

Status:  OK

CheckDir: synapter.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 synapter_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/synapter.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synapter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synapter’ version ‘1.12.0’
* 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 ‘synapter’ can be installed ... [20s/21s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.GUI: no visible global function definition for ‘tclVar’
.GUI: no visible global function definition for ‘tktoplevel’
.GUI: no visible global function definition for ‘tkbind’
.GUI : <anonymous>: no visible global function definition for
  ‘tclvalue<-’
.GUI: no visible global function definition for ‘tkwm.title’
.GUI: no visible global function definition for ‘tkframe’
.GUI: no visible global function definition for ‘tkpack’
.GUI: no visible global function definition for ‘tk2notebook’
.GUI: no visible global function definition for ‘tk2notetab’
.GUI: no visible global function definition for ‘tk2button’
.GUI : <anonymous>: no visible global function definition for
  ‘tclvalue’
.GUI : <anonymous>: no visible global function definition for ‘tcl’
.GUI : <anonymous>: no visible global function definition for
  ‘tk_choose.files’
.GUI : <anonymous>: no visible global function definition for
  ‘tkinsert’
.GUI : <anonymous>: no visible global function definition for
  ‘tk_choose.dir’
.GUI : <anonymous>: no visible global function definition for
  ‘tkdelete’
.GUI: no visible global function definition for ‘tkscrollbar’
.GUI : <anonymous>: no visible global function definition for ‘tkxview’
.GUI : <anonymous>: no visible global function definition for ‘tkyview’
.GUI: no visible global function definition for ‘tkwidget’
.GUI : <anonymous>: no visible global function definition for ‘tkset’
.GUI: no visible global function definition for ‘tkgrid’
.GUI: no visible global function definition for ‘tkgrid.configure’
.GUI: no visible global function definition for
  ‘tkgrid.columnconfigure’
.GUI: no visible global function definition for ‘tkgrid.rowconfigure’
.GUI: no visible global function definition for ‘tkinsert’
.GUI: no visible global function definition for ‘tkcheckbutton’
.GUI: no visible global function definition for ‘tkconfigure’
.GUI: no visible global function definition for ‘tklabel’
.GUI: no visible global function definition for ‘tkentry’
.GUI : <anonymous>: no visible global function definition for
  ‘tkdestroy’
.GUI: no visible global function definition for ‘tkfocus’
.GUI: no visible global function definition for ‘tkwait.variable’
synergise: no visible global function definition for ‘tk_choose.dir’
plotPepScores,Synapter : .local: no visible binding for global variable
  ‘protein.dataBaseType’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [24s/27s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
synergise 7.423  0.522  11.306
Synapter  6.558  0.263   6.844
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/synapter.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
MasterFdrResults-class	0.000	0.001	0.001
Synapter	6.558	0.263	6.844
synapterTinyData	0.136	0.011	0.146
synergise	7.423	0.522	11.306