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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:flowTrans.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings flowTrans_1.47.0.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/flowTrans.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 'flowTrans/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowTrans' version '1.47.0'
* 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 'flowTrans' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'flowCore' 'flowViz' 'flowClust'
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
Unexported object imported by a ':::' call: 'flowCore:::biexponential_transform'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'linlog'
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  summary.flowTransResult
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("_flowCore_biexponential_transform", ..., PACKAGE = "flowCore")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
flowTrans,flowFrame-character-character-logical-logical: no visible
  global function definition for 'norm2Filter'
Undefined global functions or variables:
  norm2Filter
* 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 ... NOTE
S3 methods shown with full name in documentation object 'summary.flowTransResult':
  'summary.flowTransResult'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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: 6 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/flowTrans.Rcheck/00check.log'
for details.

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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL flowTrans
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'flowTrans' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowTrans'
    finding HTML links ... done
    extractParams                           html  
    flowTrans-methods                       html  
    flowTrans-package                       html  
    flowTrans                               html  
    flowTransResult-class                   html  
    summary-methods                         html  
    summary.flowTransResult                 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
* DONE (flowTrans)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'pvac' is missing or broken
 done