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CHECK report for tkWidgets on merida2

This page was generated on 2019-04-09 13:22:14 -0400 (Tue, 09 Apr 2019).

Package 1617/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tkWidgets 1.61.0
J. Zhang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/tkWidgets
Branch: master
Last Commit: aeff0b9
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: tkWidgets
Version: 1.61.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tkWidgets.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tkWidgets_1.61.0.tar.gz
StartedAt: 2019-04-09 04:08:02 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:08:53 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 50.9 seconds
RetCode: 0
Status:  OK 
CheckDir: tkWidgets.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tkWidgets.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tkWidgets_1.61.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/tkWidgets.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tkWidgets/DESCRIPTION’ ... OK
* this is package ‘tkWidgets’ version ‘1.61.0’
* 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 ‘tkWidgets’ 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
'library' or 'require' calls to packages already attached by Depends:
  ‘DynDoc’ ‘methods’ ‘tools’ ‘widgetTools’
  Please remove these calls from your code.
'library' or 'require' call to ‘Biobase’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘DynDoc’ ‘methods’ ‘tools’ ‘widgetTools’
  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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  print.Widget print.pWidget
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘tkWidgets/R/zzz.R’:
  .onLoad calls:
    require("methods", quietly = TRUE)
    require("widgetTools", quietly = TRUE)
    require("DynDoc", quietly = TRUE)
    require(Biobase)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

.getPackNames: warning in .packages(all = TRUE): partial argument match
  of 'all' to 'all.available'
.popPackList: warning in .packages(all = TRUE): partial argument match
  of 'all' to 'all.available'
assignArgs: warning in assign("argsList", value, env = env): partial
  argument match of 'env' to 'envir'
assignLineData: warning in assign("lineData", lineData, env = env):
  partial argument match of 'env' to 'envir'
eExplorer : export: warning in assign(i, temp[[i]], env = .GlobalEnv):
  partial argument match of 'env' to 'envir'
fileWizard : view: warning in read.table(file = args$file, head =
  args$header, sep = args$sep, as.is = TRUE): partial argument match of
  'head' to 'header'
fileWizard : finish: warning in read.table(file = args$file, head =
  args$header, sep = args$sep, as.is = TRUE): partial argument match of
  'head' to 'header'
finish: warning in assign(dataName, dataFile, env = .GlobalEnv):
  partial argument match of 'env' to 'envir'
getRowNames: warning in read.table(file.name, sep = sep, nrow = 3,
  header = header, skip = skip): partial argument match of 'nrow' to
  'nrows'
objNameToList: warning in get(objNames[i], env = env): partial argument
  match of 'env' to 'envir'
objectBrowser : viewEnv: warning in ls(env = env, all = TRUE): partial
  argument match of 'env' to 'envir'
objectBrowser : viewEnv: warning in ls(env = env, all = TRUE): partial
  argument match of 'all' to 'all.names'
objectBrowser : doEnv: warning in ls(env = get(item)): partial argument
  match of 'env' to 'envir'
objectBrowser : up: warning in ls(env = get(selectedObj)): partial
  argument match of 'env' to 'envir'
viewVignette : export: warning in assign(i, temp[[i]], env =
  .GlobalEnv): partial argument match of 'env' to 'envir'
.onLoad: no visible global function definition for ‘addVigs2WinMenu’
fileWizard : brows: no visible global function definition for ‘tkcmd’
formatArg: no visible global function definition for ‘formula’
importPhenoData : getPData: no visible global function definition for
  ‘pData’
objNameToList: no visible global function definition for
  ‘package.contents’
vExplorer : write2VigList: no visible global function definition for
  ‘pkgVignettes’
Undefined global functions or variables:
  addVigs2WinMenu formula pData package.contents pkgVignettes tkcmd
Consider adding
  importFrom("stats", "formula")
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 sizes of PDF files under ‘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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/tkWidgets.Rcheck/00check.log’
for details.



Installation output

tkWidgets.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tkWidgets
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘tkWidgets’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (tkWidgets)

Tests output


Example timings

tkWidgets.Rcheck/tkWidgets-Ex.timings

nameusersystemelapsed
DPExplorer0.0000.0000.001
WName0.0040.0010.005
appendSepDir0.0010.0010.002
args2XML0.0080.0060.014
argsWidget000
colInfo-class0.0020.0010.003
dataViewer0.0000.0000.001
dbArgsWidget0.0010.0010.000
eExplorer0.0010.0000.001
fileBrowser0.0000.0000.001
fileWizard000
getLightTW0.0010.0000.001
getWvalues0.0030.0010.003
guess.sep0.0070.0010.008
hasChar000
importPhenoData000
importWizard000
listSelect0.0000.0000.001
objNameToList0.0050.0010.007
objViewer0.0010.0000.000
objectBrowser000
pExplorer0.0870.0710.161
pickFiles0.0020.0010.004
pickItems0.0010.0000.001
pickObjs0.0010.0000.002
setArgsList0.0000.0000.001
stdType0.0060.0010.008
vExplorer0.0020.0000.001
values.Widget0.0040.0010.005
widgetRender0.0010.0010.002