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CHECK report for CrispRVariants on celaya2

This page was generated on 2019-10-16 12:56:56 -0400 (Wed, 16 Oct 2019).

Package 365/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CrispRVariants 1.12.0
Helen Lindsay
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CrispRVariants
Branch: RELEASE_3_9
Last Commit: 52725a5
Last Changed Date: 2019-05-02 11:53:59 -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: CrispRVariants
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2019-10-16 01:53:23 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:00:05 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 402.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CrispRVariants.Rcheck
Warnings: 2

Command output

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### Running 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CrispRVariants.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.0’
* 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 ... 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    11.367  0.182  11.553
CrisprSet-class  7.851  0.428   8.299
mergeCrisprSets  6.962  0.200   7.165
readsToTarget    6.446  0.066   6.512
* 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-3.9-bioc/meat/CrispRVariants.Rcheck/00check.log’
for details.



Installation output

CrispRVariants.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CrispRVariants
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CrispRVariants’ ...
** using staged installation
** 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 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 (CrispRVariants)

Tests output

CrispRVariants.Rcheck/tests/testthat.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-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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 36.102   2.002  38.066 

Example timings

CrispRVariants.Rcheck/CrispRVariants-Ex.timings

nameusersystemelapsed
CrisprRun-class1.6620.0161.680
CrisprSet-class7.8510.4288.299
abifToFastq0.3530.0190.377
alleles0.2410.0160.257
alns0.2410.0140.255
barplotAlleleFreqs1.5910.0351.626
consensusSeqs0.8150.0200.834
dispatchDots0.0040.0000.005
findChimeras0.0460.0020.050
getChimeras0.0650.0050.070
indelCounts0.1680.0010.169
intersperse0.0000.0000.001
mergeCrisprSets6.9620.2007.165
mutationEfficiency0.0550.0050.060
narrowAlignments0.4550.0030.459
plotAlignments1.3230.0221.346
plotChimeras1.6630.0051.670
plotFreqHeatmap0.5060.0070.514
plotVariants11.367 0.18211.553
readsToTarget6.4460.0666.512
selectAlnRegionsHelpers0.0010.0000.001
variantCounts0.0520.0040.056