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CHECK report for CrispRVariants on malbec1

This page was generated on 2019-04-16 11:51:46 -0400 (Tue, 16 Apr 2019).

Package 346/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CrispRVariants 1.10.1
Helen Lindsay
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/CrispRVariants
Branch: RELEASE_3_8
Last Commit: 8269b06
Last Changed Date: 2019-01-04 13:27:32 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CrispRVariants
Version: 1.10.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CrispRVariants_1.10.1.tar.gz
StartedAt: 2019-04-15 23:14:01 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:18:12 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 251.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CrispRVariants.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CrispRVariants_1.10.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/CrispRVariants.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 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 7.236  0.112   7.382
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/CrispRVariants.Rcheck/00check.log’
for details.



Installation output

CrispRVariants.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL CrispRVariants
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output

CrispRVariants.Rcheck/tests/testthat.Rout


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

> 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 
 23.744   0.420  24.223 

Example timings

CrispRVariants.Rcheck/CrispRVariants-Ex.timings

nameusersystemelapsed
CrisprRun-class0.5080.0160.533
CrisprSet-class4.4120.0164.483
abifToFastq0.1760.0040.194
alleles0.1920.0000.192
alns0.720.000.72
barplotAlleleFreqs1.0280.0001.031
consensusSeqs0.3360.0040.341
dispatchDots0.0000.0000.002
findChimeras0.0440.0000.043
getChimeras0.0440.0000.044
indelCounts0.140.000.14
intersperse000
mergeCrisprSets4.7320.0044.740
mutationEfficiency0.0520.0000.052
narrowAlignments0.2760.0000.275
plotAlignments0.7800.0000.782
plotChimeras1.4200.0001.426
plotFreqHeatmap0.4920.0000.491
plotVariants7.2360.1127.382
readsToTarget4.0000.0164.026
selectAlnRegionsHelpers0.0040.0000.001
variantCounts0.0440.0000.044