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This page was generated on 2022-01-20 11:10:48 -0500 (Thu, 20 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4162
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4057
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3999
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4116
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for CrispRVariants on merida1


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 420/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CrispRVariants 1.23.0  (landing page)
Helen Lindsay
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/CrispRVariants
git_branch: master
git_last_commit: d8ef937
git_last_commit_date: 2021-10-26 12:24:29 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CrispRVariants
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CrispRVariants_1.23.0.tar.gz
StartedAt: 2022-01-19 23:45:10 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 23:52:30 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 439.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CrispRVariants.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CrispRVariants_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CrispRVariants.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.23.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
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 ‘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 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 (user + system) or elapsed time > 5s
                  user system elapsed
plotVariants    11.716  0.190  11.921
CrisprSet-class  7.931  0.175   8.119
mergeCrisprSets  7.295  0.038   7.341
readsToTarget    6.753  0.045   6.806
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/CrispRVariants.Rcheck/00check.log’
for details.



Installation output

CrispRVariants.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
 41.733   1.002  42.767 

Example timings

CrispRVariants.Rcheck/CrispRVariants-Ex.timings

nameusersystemelapsed
CrisprRun-class1.0220.0631.088
CrisprSet-class7.9310.1758.119
abifToFastq0.4460.0130.461
alleles0.8960.0100.907
alns0.1530.0040.158
barplotAlleleFreqs1.3610.0171.381
consensusSeqs0.6500.0040.655
dispatchDots0.0030.0000.003
findChimeras0.0440.0010.047
getChimeras0.0500.0010.052
indelCounts0.1550.0030.158
intersperse0.0000.0000.001
mergeCrisprSets7.2950.0387.341
mutationEfficiency0.0650.0020.067
narrowAlignments0.4800.0020.483
plotAlignments1.2500.0071.259
plotChimeras1.9290.0061.936
plotFreqHeatmap0.4770.0050.483
plotVariants11.716 0.19011.921
readsToTarget6.7530.0456.806
selectAlnRegionsHelpers000
variantCounts0.0720.0010.074