Package: tkWidgets

Version: 1.61.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tkWidgets.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings tkWidgets_1.61.0.tar.gz

StartedAt: 2019-04-09 06:21:44 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 06:22:56 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 71.9 seconds

RetCode: 0

Status:  OK

CheckDir: tkWidgets.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tkWidgets.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings tkWidgets_1.61.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/tkWidgets.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.61.0'
* 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 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 ... 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'
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 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/tkWidgets.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/tkWidgets_1.61.0.tar.gz && rm -rf tkWidgets.buildbin-libdir && mkdir tkWidgets.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tkWidgets.buildbin-libdir tkWidgets_1.61.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL tkWidgets_1.61.0.zip && rm tkWidgets_1.61.0.tar.gz tkWidgets_1.61.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  180k  100  180k    0     0  3160k      0 --:--:-- --:--:-- --:--:-- 3543k

install for i386

* installing *source* package 'tkWidgets' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'tkWidgets'
    finding HTML links ... done
    DPExplorer                              html  
    WName                                   html  
    appendSepDir                            html  
    args2XML                                html  
    argsWidget                              html  
    colInfo-class                           html  
    dataViewer                              html  
    dbArgsWidget                            html  
    eExplorer                               html  
    fileBrowser                             html  
    fileWizard                              html  
    getLightTW                              html  
    getWvalues                              html  
    guess.sep                               html  
    hasChar                                 html  
    importPhenoData                         html  
    importWizard                            html  
    listSelect                              html  
    objNameToList                           html  
    objViewer                               html  
    objectBrowser                           html  
    pExplorer                               html  
    pickFiles                               html  
    pickItems                               html  
    pickObjs                                html  
    setArgsList                             html  
    stdType                                 html  
    tkMIAME                                 html  
    tkSampleNames                           html  
    tkphenoData                             html  
    vExplorer                               html  
    values.Widget                           html  
    widgetRender                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'tkWidgets' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tkWidgets' as tkWidgets_1.61.0.zip
* DONE (tkWidgets)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'tkWidgets' successfully unpacked and MD5 sums checked