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BioC 3.5: CHECK report for tkWidgets on tokay2

This page was generated on 2017-08-16 13:18:29 -0400 (Wed, 16 Aug 2017).

Package 1321/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tkWidgets 1.54.0
J. Zhang
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/tkWidgets
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -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: rm -rf tkWidgets.buildbin-libdir tkWidgets.Rcheck && mkdir tkWidgets.buildbin-libdir tkWidgets.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=tkWidgets.buildbin-libdir tkWidgets_1.54.0.tar.gz >tkWidgets.Rcheck\00install.out 2>&1 && cp tkWidgets.Rcheck\00install.out tkWidgets-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=tkWidgets.buildbin-libdir --install="check:tkWidgets-install.out" --force-multiarch --no-vignettes --timings tkWidgets_1.54.0.tar.gz
StartedAt: 2017-08-16 03:18:38 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:19:47 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 68.6 seconds
RetCode: 0
Status:  OK  
CheckDir: tkWidgets.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf tkWidgets.buildbin-libdir tkWidgets.Rcheck && mkdir tkWidgets.buildbin-libdir tkWidgets.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=tkWidgets.buildbin-libdir tkWidgets_1.54.0.tar.gz >tkWidgets.Rcheck\00install.out 2>&1 && cp tkWidgets.Rcheck\00install.out tkWidgets-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=tkWidgets.buildbin-libdir --install="check:tkWidgets-install.out" --force-multiarch --no-vignettes --timings tkWidgets_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/tkWidgets.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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
'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'
fileWizard : brows: no visible global function definition for 'tkcmd'
objNameToList: no visible global function definition for
  'package.contents'
vExplorer : write2VigList: no visible global function definition for
  'pkgVignettes'
Undefined global functions or variables:
  package.contents pkgVignettes tkcmd
* 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-3.5-bioc/meat/tkWidgets.Rcheck/00check.log'
for details.


tkWidgets.Rcheck/00install.out:


install for i386

* installing *source* package 'tkWidgets' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'tkWidgets' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tkWidgets' as tkWidgets_1.54.0.zip
* DONE (tkWidgets)

tkWidgets.Rcheck/examples_i386/tkWidgets-Ex.timings:

nameusersystemelapsed
DPExplorer000
WName0.020.000.02
appendSepDir000
args2XML0.010.000.01
argsWidget0.020.000.02
colInfo-class000
dataViewer000
dbArgsWidget000
eExplorer000
fileBrowser000
fileWizard0.010.000.01
getLightTW000
getWvalues000
guess.sep0.020.000.02
hasChar000
importPhenoData000
importWizard000
listSelect000
objNameToList0.010.000.01
objViewer000
objectBrowser000
pExplorer0.050.100.14
pickFiles0.020.000.02
pickItems000
pickObjs000
setArgsList000
stdType0.010.000.02
vExplorer000
values.Widget000
widgetRender000

tkWidgets.Rcheck/examples_x64/tkWidgets-Ex.timings:

nameusersystemelapsed
DPExplorer000
WName0.010.000.02
appendSepDir000
args2XML0.010.000.02
argsWidget000
colInfo-class000
dataViewer000
dbArgsWidget000
eExplorer000
fileBrowser000
fileWizard000
getLightTW000
getWvalues000
guess.sep0.020.000.01
hasChar000
importPhenoData000
importWizard000
listSelect0.010.000.02
objNameToList000
objViewer000
objectBrowser0.020.000.02
pExplorer0.050.090.14
pickFiles0.010.000.01
pickItems0.020.000.02
pickObjs000
setArgsList000
stdType0.010.000.01
vExplorer000
values.Widget000
widgetRender000