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This page was generated on 2023-10-20 09:38:01 -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 601/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DynDoc 1.78.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/DynDoc
git_branch: RELEASE_3_17
git_last_commit: 222aae6
git_last_commit_date: 2023-04-25 09:38:12 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for DynDoc on kjohnson2


To the developers/maintainers of the DynDoc 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: DynDoc
Version: 1.78.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DynDoc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DynDoc_1.78.0.tar.gz
StartedAt: 2023-10-17 17:02:01 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 17:02:43 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 41.5 seconds
RetCode: 0
Status:   OK  
CheckDir: DynDoc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DynDoc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DynDoc_1.78.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DynDoc.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 ‘DynDoc/DESCRIPTION’ ... OK
* this is package ‘DynDoc’ 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 ‘DynDoc’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘DynDoc/R/zzz.R’:
  .onLoad has wrong argument list ‘pkgname, libname’
  .onLoad calls:
    require("methods")

Package startup functions should have two arguments with names starting
  with ‘lib’ and ‘pkg’, respectively.
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

getVignette: no visible global function definition for ‘Stangle’
getVignette: no visible global function definition for
  ‘buildVersionNumber’
getVignette: no visible global function definition for
  ‘installed.packages’
getVignette: no visible global function definition for
  ‘package.description’
getVignetteCode: no visible global function definition for ‘Stangle’
tangleToR: no visible binding for global variable ‘RtangleWritedoc’
tangleToR: no visible binding for global variable ‘RweaveLatexOptions’
Undefined global functions or variables:
  RtangleWritedoc RweaveLatexOptions Stangle buildVersionNumber
  installed.packages package.description
Consider adding
  importFrom("utils", "RtangleWritedoc", "RweaveLatexOptions", "Stangle",
             "installed.packages")
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 examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DynDoc.Rcheck/00check.log’
for details.



Installation output

DynDoc.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DynDoc
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘DynDoc’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (DynDoc)

Tests output


Example timings

DynDoc.Rcheck/DynDoc-Ex.timings

nameusersystemelapsed
chunkList-class0.0410.0050.064
codeChunk-class0.0160.0010.025
getPkgVigList000
tangleToR0.0210.0010.032