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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DynDoc.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DynDoc_1.73.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/DynDoc.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DynDoc/DESCRIPTION' ... OK
* this is package 'DynDoc' version '1.73.0'
* 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 '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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/DynDoc.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DynDoc
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'DynDoc' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DynDoc'
    finding HTML links ... done
    DynDoc-class                            html  
    SweaveOptions-class                     html  
    Vignette-class                          html  
    chunkList-class                         html  
    codeChunk-class                         html  
    getPkgVigList                           html  
    getVignette                             html  
    getVignetteCode                         html  
    getVignetteHeader                       html  
    tangleToR                               html  
    vignetteCode-class                      html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ISoLDE' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'swfdr' is missing or broken
 done