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This page was generated on 2021-09-13 15:05:57 -0400 (Mon, 13 Sep 2021).

CHECK results for CrispRVariants on nebbiolo1

To the developers/maintainers of the CrispRVariants package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CrispRVariants.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 411/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CrispRVariants 1.20.0  (landing page)
Helen Lindsay
Snapshot Date: 2021-09-12 04:50:10 -0400 (Sun, 12 Sep 2021)
git_url: https://git.bioconductor.org/packages/CrispRVariants
git_branch: RELEASE_3_13
git_last_commit: 6789cce
git_last_commit_date: 2021-05-19 12:17:13 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CrispRVariants
Version: 1.20.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CrispRVariants_1.20.0.tar.gz
StartedAt: 2021-09-12 09:24:20 -0400 (Sun, 12 Sep 2021)
EndedAt: 2021-09-12 09:28:14 -0400 (Sun, 12 Sep 2021)
EllapsedTime: 233.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CrispRVariants.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CrispRVariants_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CrispRVariants.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.20.0’
* 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 LazyData ... 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 (user + system) or elapsed time > 5s
              user system elapsed
plotVariants 6.434   0.06   6.495
* 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-3.13-bioc/meat/CrispRVariants.Rcheck/00check.log’
for details.



Installation output

CrispRVariants.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CrispRVariants
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
 23.005   0.906  23.898 

Example timings

CrispRVariants.Rcheck/CrispRVariants-Ex.timings

nameusersystemelapsed
CrisprRun-class0.5460.0610.606
CrisprSet-class3.9710.1394.113
abifToFastq0.2000.0120.212
alleles0.1110.0000.111
alns0.0780.0080.085
barplotAlleleFreqs0.6640.0080.672
consensusSeqs1.0070.0001.007
dispatchDots0.0020.0000.002
findChimeras0.0280.0030.032
getChimeras0.0260.0000.025
indelCounts0.0930.0160.109
intersperse0.0010.0000.000
mergeCrisprSets3.7450.0163.761
mutationEfficiency0.0270.0040.031
narrowAlignments0.2390.0120.250
plotAlignments0.5940.0080.602
plotChimeras1.0170.0121.029
plotFreqHeatmap0.2140.0040.219
plotVariants6.4340.0606.495
readsToTarget3.6670.0483.716
selectAlnRegionsHelpers000
variantCounts0.0260.0030.030