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CHECK report for VariantTools on malbec2

This page was generated on 2019-10-16 12:01:52 -0400 (Wed, 16 Oct 2019).

Package 1708/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantTools 1.26.0
Michael Lawrence
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/VariantTools
Branch: RELEASE_3_9
Last Commit: 780ffb6
Last Changed Date: 2019-05-02 11:53:39 -0400 (Thu, 02 May 2019)
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

Summary

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

Command output

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### Running 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
###
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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.



Installation output

VariantTools.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output

VariantTools.Rcheck/tests/VariantTools_unit_tests.Rout


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 

Example timings

VariantTools.Rcheck/VariantTools-Ex.timings

nameusersystemelapsed
FilterConstructors1.4270.0922.039
annnotateWithControlDepth0.4850.0160.501
callGenotypes75.90011.91860.697
callSampleSpecificVariants7.7245.8906.422
callVariants3.9042.9563.142
callWildtype0.3550.0120.368
pileupVariants0.2420.2720.514
postFilterVariants0.2420.0200.261
qaVariants0.1460.0160.161
tallyVariants3.1942.3542.882
variantGR2Vcf000
vignette0.6530.6200.027