##############################################################################
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###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VariantTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings VariantTools_1.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/VariantTools.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 'VariantTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VariantTools' version '1.37.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'gmapR'
* 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:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'VariantTools' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'IRanges:::unlist_as_integer'
  See the note in ?`:::` about the use of this operator.
Unavailable namespace imported from by a ':::' call: 'gmapR'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
  global variable 'control.alt.depth'
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
  global variable 'control.total.depth'
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable 'read.pos.mean'
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable 'read.pos.mean.ref'
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable 'read.pos.var'
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable 'read.pos.var.ref'
ReadPositionTTestFilter : <anonymous>: no visible global function
  definition for 'rawDepth'
StrandFETFilter : <anonymous>: no visible binding for global variable
  'count.plus.ref'
StrandFETFilter : <anonymous>: no visible binding for global variable
  'count.minus.ref'
StrandFETFilter : <anonymous>: no visible binding for global variable
  'count.plus'
StrandFETFilter : <anonymous>: no visible binding for global variable
  'count.minus'
calculateConcordanceMatrix: no visible binding for global variable 'x'
caseControlFET: no visible binding for global variable
  'control.alt.depth'
caseControlFET: no visible binding for global variable
  'control.total.depth'
variantGR2Vcf: no visible global function definition for
  'variantGRangesIsDeprecated'
variantGR2Vcf: no visible global function definition for
  'makeVRangesFromVariantGRanges'
callVariants,GenomicRanges: no visible global function definition for
  'variantGRangesIsDeprecated'
callVariants,GenomicRanges: no visible global function definition for
  'variantGRangesToVRanges'
Undefined global functions or variables:
  control.alt.depth control.total.depth count.minus count.minus.ref
  count.plus count.plus.ref makeVRangesFromVariantGRanges rawDepth
  read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref
  variantGRangesIsDeprecated variantGRangesToVRanges x
* checking Rd files ... WARNING
man/tallyVariants.Rd: non-ASCII input and no declared encoding
problem found in 'tallyVariants.Rd'
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'gmapR'
* 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 installed files from 'inst/doc' ... NOTE
The following directories should probably not be installed:
  'fig'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
callGenotypes 2.17   0.08   25.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'VariantTools_unit_tests.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 WARNING, 7 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/VariantTools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL VariantTools
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'VariantTools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'VariantTools'
    finding HTML links ... done
    FilterConstructors                      html  
    annnotateWithControlDepth               html  
    callGenotypes                           html  
    callSampleSpecificVariants              html  
    callVariants                            html  
    callWildtype                            html  
    concordance                             html  
    extractCoverageForPositions             html  
    matchVariants                           html  
    pileupVariants                          html  
    postFilterVariants                      html  
    qaVariants                              html  
    tallyVariants                           html  
    finding level-2 HTML links ... done

    variantGR2Vcf                           html  
    vignette                                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 (VariantTools)
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.

> ##require("VariantTools") || stop("unable to load VariantTools package")
> ##VariantTools:::.test()
> 
> proc.time()
   user  system elapsed 
   0.15    0.03    0.14