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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scanMiR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scanMiR_1.1.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/scanMiR.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 'scanMiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scanMiR' version '1.1.0'
* 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 'scanMiR' 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
.aggregateSiteInfo: no visible binding for global variable 'ORF'
.aggregateSiteInfo: no visible global function definition for '.'
.aggregateSiteInfo: no visible binding for global variable
  'ORF.canonical'
.aggregateSiteInfo: no visible binding for global variable '..cols'
.aggregate_miRNA: no visible binding for global variable 'ORF'
.aggregate_miRNA: no visible binding for global variable 'log_kd'
.aggregate_miRNA: no visible binding for global variable 'orf.length'
.aggregate_miRNA: no visible binding for global variable 'utr.length'
.aggregate_miRNA: no visible binding for global variable 'utr_score'
.aggregate_miRNA: no visible binding for global variable 'orf_score'
dummyKdData: no visible binding for global variable 'SampleKdModel'
plotKdModel: no visible binding for global variable 'seed'
plotKdModel: no visible binding for global variable 'log_kd'
viewTargetAlignment: no visible binding for global variable 'x'
viewTargetAlignment: no visible binding for global variable 'y'
viewTargetAlignment: no visible binding for global variable 'label'
Undefined global functions or variables:
  . ..cols ORF ORF.canonical SampleKdModel label log_kd orf.length
  orf_score seed utr.length utr_score x y
* 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/scanMiR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL scanMiR
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'scanMiR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scanMiR'
    finding HTML links ... done
    KdModel                                 html  
    KdModelList-methods                     html  
    KdModelList                             html  
    SampleKdModel                           html  
    SampleTranscript                        html  
    aggregateMatches                        html  
    finding level-2 HTML links ... done

    assignKdType                            html  
    conservation                            html  
    dummyKdData                             html  
    findSeedMatches                         html  
    get3pAlignment                          html  
    get8merRange                            html  
    getKdModel                              html  
    getKmers                                html  
    getMatchTypes                           html  
    getRandomSeq                            html  
    getSeed8mers                            html  
    plotKdModel                             html  
    removeOverlappingRanges                 html  
    viewTargetAlignment                     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 (scanMiR)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scanMiR)
> 
> test_check("scanMiR")
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 76 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 76 ]
> 
> proc.time()
   user  system elapsed 
   9.20    0.32    9.48