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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:SynExtend.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SynExtend_1.7.11.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/SynExtend.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 'SynExtend/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SynExtend' version '1.7.11'
* package encoding: UTF-8
* 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 'SynExtend' 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BlockExpansion: no visible global function definition for
  'ScoreAlignment'
PairSummaries: no visible global function definition for
  'ScoreAlignment'
Undefined global functions or variables:
  ScoreAlignment
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
BlockExpansion 101.11  13.83  114.94
gffToDataFrame  28.13   0.48   28.61
PairSummaries    6.15   2.44    8.59
* 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/SynExtend.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 SynExtend
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'SynExtend' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SynExtend'
    finding HTML links ... done
    BlockExpansion                          html  
    finding level-2 HTML links ... done

    BlockReconciliation                     html  
    DisjointSet                             html  
    EstimateRearrangementScenarios          html  
    ExtractBy                               html  
    FindSets                                html  
    Generic                                 html  
    LinkedPairs-class                       html  
    Nitrosocosmicus_GeneCalls               html  
    Nitrosocosmicus_LinkedFeatures          html  
    Nitrosocosmicus_Pairs01                 html  
    Nitrosocosmicus_Pairs02                 html  
    Nitrosocosmicus_Pairs03                 html  
    Nitrosocosmicus_Sets                    html  
    Nitrosocosmicus_Synteny                 html  
    NucleotideOverlap                       html  
    PairSummaries                           html  
    SequenceSimilarity                      html  
    SubSetPairs                             html  
    gffToDataFrame                          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 (SynExtend)
Making 'packages.html' ... done