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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2105/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tkWidgets 1.78.0  (landing page)
J. Zhang
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/tkWidgets
git_branch: RELEASE_3_17
git_last_commit: 2e5bf44
git_last_commit_date: 2023-04-25 09:38:34 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for tkWidgets on kjohnson2


To the developers/maintainers of the tkWidgets package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: tkWidgets
Version: 1.78.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tkWidgets.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tkWidgets_1.78.0.tar.gz
StartedAt: 2023-10-19 07:09:53 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 07:11:25 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 91.9 seconds
RetCode: 0
Status:   OK  
CheckDir: tkWidgets.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tkWidgets.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tkWidgets_1.78.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/tkWidgets.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tkWidgets/DESCRIPTION’ ... OK
* this is package ‘tkWidgets’ version ‘1.78.0’
* 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 startup messages can be suppressed ... 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/tkWidgets.Rcheck/00check.log’
for details.



Installation output

tkWidgets.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tkWidgets
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘tkWidgets’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tkWidgets)

Tests output


Example timings

tkWidgets.Rcheck/tkWidgets-Ex.timings

nameusersystemelapsed
DPExplorer000
WName0.0020.0010.007
appendSepDir0.0010.0000.010
args2XML0.0050.0070.021
argsWidget000
colInfo-class0.0010.0010.002
dataViewer000
dbArgsWidget0.0000.0000.001
eExplorer0.0000.0000.001
fileBrowser0.0000.0010.001
fileWizard0.0010.0000.003
getLightTW000
getWvalues0.0020.0010.005
guess.sep0.0050.0020.013
hasChar0.0000.0000.001
importPhenoData000
importWizard0.0000.0010.000
listSelect0.0010.0000.001
objNameToList0.0050.0000.014
objViewer0.0010.0000.000
objectBrowser000
pExplorer0.0350.0650.182
pickFiles0.0010.0020.003
pickItems000
pickObjs0.0010.0000.001
setArgsList0.0000.0010.000
stdType0.0040.0010.006
vExplorer0.0000.0000.001
values.Widget0.0090.0010.015
widgetRender0.0000.0010.005