Package: CrispRVariants

Version: 1.10.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CrispRVariants_1.10.1.tar.gz

StartedAt: 2019-04-15 23:17:17 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:22:02 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 285.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CrispRVariants.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CrispRVariants_1.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CrispRVariants.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CrispRVariants/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CrispRVariants’ version ‘1.10.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CrispRVariants’ 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 ... WARNING
'::' or ':::' import not declared from: ‘SummarizedExperiment’
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘indelLabels’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'arrangePlots':
arrangePlots
  Code: function(top.plot, left.plot, right.plot, fig.height = NULL,
                 col.wdth.ratio = c(2, 1), row.ht.ratio = c(1, 6),
                 left.plot.margin = grid::unit(c(0.1, 0.2, 3, 0.2),
                 "lines"))
  Docs: function(top.plot, left.plot, right.plot, fig.height = NULL,
                 col.wdth.ratio = c(2, 1), row.ht.ratio = c(1, 6),
                 left.plot.margin = grid::unit(c(0.1, 0, 3, 0.2),
                 "lines"))
  Mismatches in argument default values:
    Name: 'left.plot.margin' Code: grid::unit(c(0.1, 0.2, 3, 0.2), "lines") Docs: grid::unit(c(0.1, 0, 3, 0.2), "lines")

Codoc mismatches from documentation object 'indelLabels':
indelLabels
  Code: function(alns, rc = FALSE, genome.to.pos = NULL, keep.ops =
                 c("I", "D", "N"), regions = NULL, as.string = TRUE,
                 ...)
  Docs: function(alns, rc = FALSE, genome.to.pos = NULL, keep.ops =
                 c("I", "D", "N"), regions = NULL, ...)
  Argument names in code not in docs:
    as.string
  Mismatches in argument names:
    Position: 6 Code: as.string Docs: ...

* 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotVariants    8.011  0.265   8.339
CrisprSet-class 5.558  0.059   5.684
mergeCrisprSets 5.404  0.063   5.511
* 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: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/CrispRVariants.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CrispRVariants
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CrispRVariants’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CrispRVariants)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> library(testthat)
> test_check("CrispRVariants")
Loading required package: CrispRVariants
Loading required package: ggplot2
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 75 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 28.143   0.905  29.296 

name	user	system	elapsed
CrisprRun-class	0.821	0.056	0.888
CrisprSet-class	5.558	0.059	5.684
abifToFastq	0.254	0.009	0.268
alleles	0.236	0.005	0.243
alns	0.771	0.013	0.797
barplotAlleleFreqs	1.235	0.023	1.269
consensusSeqs	0.560	0.011	0.575
dispatchDots	0.004	0.000	0.004
findChimeras	0.041	0.001	0.043
getChimeras	0.038	0.003	0.041
indelCounts	0.118	0.002	0.121
intersperse	0.000	0.000	0.001
mergeCrisprSets	5.404	0.063	5.511
mutationEfficiency	0.039	0.002	0.042
narrowAlignments	0.345	0.002	0.350
plotAlignments	0.995	0.014	1.017
plotChimeras	1.472	0.008	1.495
plotFreqHeatmap	0.491	0.004	0.498
plotVariants	8.011	0.265	8.339
readsToTarget	4.536	0.059	4.624
selectAlnRegionsHelpers	0.001	0.000	0.001
variantCounts	0.042	0.004	0.047