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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).

CHECK results for DynDoc on machv2

To the developers/maintainers of the DynDoc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DynDoc.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 543/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DynDoc 1.70.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/DynDoc
git_branch: RELEASE_3_13
git_last_commit: fcb8530
git_last_commit_date: 2021-05-19 11:32:32 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DynDoc
Version: 1.70.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DynDoc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DynDoc_1.70.0.tar.gz
StartedAt: 2021-10-14 18:38:06 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 18:38:35 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 28.5 seconds
RetCode: 0
Status:   OK  
CheckDir: DynDoc.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DynDoc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DynDoc_1.70.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/DynDoc.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DynDoc/DESCRIPTION’ ... OK
* this is package ‘DynDoc’ version ‘1.70.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/DynDoc.Rcheck/00check.log’
for details.



Installation output

DynDoc.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DynDoc
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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-class0.0400.0040.045
codeChunk-class0.0230.0010.024
getPkgVigList000
tangleToR0.0180.0000.019