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BioC 3.5: CHECK report for tkWidgets on malbec2

This page was generated on 2017-10-18 14:12:14 -0400 (Wed, 18 Oct 2017).

Package 1320/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tkWidgets 1.54.0
J. Zhang
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/tkWidgets
Branch: RELEASE_3_5
Last Commit: eadf91e
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: tkWidgets
Version: 1.54.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings tkWidgets_1.54.0.tar.gz
StartedAt: 2017-10-18 02:54:42 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:55:13 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 30.7 seconds
RetCode: 0
Status:  OK 
CheckDir: tkWidgets.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings tkWidgets_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/tkWidgets.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.54.0’
* 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 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/tkWidgets.Rcheck/00check.log’
for details.


tkWidgets.Rcheck/00install.out:

* installing *source* package ‘tkWidgets’ ...
** R
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
* DONE (tkWidgets)

tkWidgets.Rcheck/tkWidgets-Ex.timings:

nameusersystemelapsed
DPExplorer0.0000.0000.001
WName0.0040.0000.005
appendSepDir0.0000.0000.002
args2XML0.0040.0080.012
argsWidget0.0000.0000.001
colInfo-class0.0000.0000.002
dataViewer0.0000.0000.001
dbArgsWidget0.0040.0000.001
eExplorer0.0000.0000.001
fileBrowser0.0040.0000.002
fileWizard0.0000.0000.001
getLightTW0.0000.0000.001
getWvalues0.0040.0000.003
guess.sep0.0080.0040.010
hasChar0.0040.0000.001
importPhenoData0.0000.0000.001
importWizard0.0000.0000.001
listSelect0.0040.0000.001
objNameToList0.0120.0000.010
objViewer0.0000.0000.001
objectBrowser0.0000.0000.001
pExplorer0.0520.0160.065
pickFiles0.0240.0000.023
pickItems0.0000.0000.001
pickObjs0.0000.0000.002
setArgsList0.0000.0000.001
stdType0.0080.0000.007
vExplorer0.0040.0000.001
values.Widget0.0040.0000.004
widgetRender0.0040.0000.002