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CHECK report for VariantTools on merida2

This page was generated on 2019-04-09 13:27:37 -0400 (Tue, 09 Apr 2019).

Package 1671/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantTools 1.25.1
Michael Lawrence
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/VariantTools
Branch: master
Last Commit: a96f99b
Last Changed Date: 2018-12-05 13:01:28 -0400 (Wed, 05 Dec 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: VariantTools
Version: 1.25.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings VariantTools_1.25.1.tar.gz
StartedAt: 2019-04-09 04:20:17 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:26:07 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 349.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: VariantTools.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings VariantTools_1.25.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/VariantTools.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.25.1’
* 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 : <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 ... 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 sizes of PDF files under ‘inst/doc’ ... 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              83.661  9.721  53.203
callSampleSpecificVariants  9.129  6.424   5.428
callVariants                4.389  3.118   2.615
tallyVariants               4.139  3.105   2.201
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/VariantTools.Rcheck/00check.log’
for details.



Installation output

VariantTools.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL VariantTools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘VariantTools’ ...
** 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
* DONE (VariantTools)

Tests output

VariantTools.Rcheck/tests/VariantTools_unit_tests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
  0.272   0.076   0.316 

Example timings

VariantTools.Rcheck/VariantTools-Ex.timings

nameusersystemelapsed
FilterConstructors1.4000.1001.511
annnotateWithControlDepth1.1420.0071.159
callGenotypes83.661 9.72153.203
callSampleSpecificVariants9.1296.4245.428
callVariants4.3893.1182.615
callWildtype0.3960.0430.442
pileupVariants0.2640.0480.318
postFilterVariants0.3120.0050.323
qaVariants0.2390.0190.265
tallyVariants4.1393.1052.201
variantGR2Vcf0.0000.0010.001
vignette0.0170.0060.023