Package: tkWidgets

Version: 1.60.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:tkWidgets.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings tkWidgets_1.60.0.tar.gz

StartedAt: 2019-04-16 03:26:21 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:26:51 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 30.9 seconds

RetCode: 0

Status:  OK

CheckDir: tkWidgets.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:tkWidgets.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings tkWidgets_1.60.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/tkWidgets.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tkWidgets/DESCRIPTION’ ... OK
* this is package ‘tkWidgets’ version ‘1.60.0’
* 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 ... OK
* 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 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/tkWidgets.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL tkWidgets
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

name	user	system	elapsed
DPExplorer	0.000	0.000	0.001
WName	0.000	0.004	0.002
appendSepDir	0.004	0.000	0.001
args2XML	0.012	0.000	0.014
argsWidget	0.000	0.000	0.001
colInfo-class	0.000	0.000	0.002
dataViewer	0	0	0
dbArgsWidget	0.000	0.000	0.001
eExplorer	0.000	0.000	0.001
fileBrowser	0.000	0.000	0.001
fileWizard	0	0	0
getLightTW	0	0	0
getWvalues	0.004	0.000	0.003
guess.sep	0.000	0.008	0.009
hasChar	0.004	0.000	0.001
importPhenoData	0	0	0
importWizard	0.000	0.000	0.001
listSelect	0.000	0.000	0.001
objNameToList	0.000	0.004	0.007
objViewer	0	0	0
objectBrowser	0	0	0
pExplorer	0.052	0.028	0.110
pickFiles	0.004	0.000	0.002
pickItems	0	0	0
pickObjs	0.000	0.000	0.001
setArgsList	0	0	0
stdType	0.004	0.000	0.006
vExplorer	0.004	0.000	0.000
values.Widget	0.000	0.000	0.002
widgetRender	0.000	0.000	0.001