Package: VariantTools

Version: 1.26.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings VariantTools_1.26.0.tar.gz

StartedAt: 2019-10-16 05:40:26 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:46:10 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 344.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: VariantTools.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings VariantTools_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/VariantTools.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantTools’ version ‘1.26.0’
* 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 ... 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 for sufficient/correct file permissions ... OK
* checking whether package ‘VariantTools’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  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’
  ‘gmapR:::showSlots’
  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 : : no visible binding for
  global variable ‘control.alt.depth’
LowerFrequencyInOtherFilter : : no visible binding for
  global variable ‘control.total.depth’
ReadPositionTTestFilter : : no visible binding for global
  variable ‘read.pos.mean’
ReadPositionTTestFilter : : no visible binding for global
  variable ‘read.pos.mean.ref’
ReadPositionTTestFilter : : no visible binding for global
  variable ‘read.pos.var’
ReadPositionTTestFilter : : no visible binding for global
  variable ‘read.pos.var.ref’
ReadPositionTTestFilter : : no visible global function
  definition for ‘rawDepth’
StrandFETFilter : : no visible binding for global variable
  ‘count.plus.ref’
StrandFETFilter : : no visible binding for global variable
  ‘count.minus.ref’
StrandFETFilter : : no visible binding for global variable
  ‘count.plus’
StrandFETFilter : : 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 ... 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 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 or elapsed time > 5s
                             user system elapsed
callGenotypes              75.900 11.918  60.697
callSampleSpecificVariants  7.724  5.890   6.422
callVariants                3.904  2.956   3.142
tallyVariants               3.194  2.354   2.882
* 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, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/VariantTools.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL VariantTools
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* installing to library ‘/home/biocbuild/bbs-3.9-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
** building package indices
** installing vignettes
   ‘VariantTools.Rnw’ 
** 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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.243   0.032   0.261 

name	user	system	elapsed
FilterConstructors	1.427	0.092	2.039
annnotateWithControlDepth	0.485	0.016	0.501
callGenotypes	75.900	11.918	60.697
callSampleSpecificVariants	7.724	5.890	6.422
callVariants	3.904	2.956	3.142
callWildtype	0.355	0.012	0.368
pileupVariants	0.242	0.272	0.514
postFilterVariants	0.242	0.020	0.261
qaVariants	0.146	0.016	0.161
tallyVariants	3.194	2.354	2.882
variantGR2Vcf	0	0	0
vignette	0.653	0.620	0.027