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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 461/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CrispRVariants 1.34.0  (landing page)
Helen Lindsay
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CrispRVariants
git_branch: RELEASE_3_20
git_last_commit: 95baa0b
git_last_commit_date: 2024-10-29 10:06:09 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for CrispRVariants on nebbiolo2

To the developers/maintainers of the CrispRVariants package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CrispRVariants
Version: 1.34.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CrispRVariants_1.34.0.tar.gz
StartedAt: 2024-12-19 22:07:24 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 22:17:08 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 584.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CrispRVariants.Rcheck
Warnings: 2

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CrispRVariants_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CrispRVariants.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CrispRVariants/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CrispRVariants’ version ‘1.34.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 loading without being on the library search path ... 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 ... OK
* 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 (user + system) or elapsed time > 5s
              user system elapsed
plotVariants 6.316  0.223   6.539
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘gdata’
'library' or 'require' call not declared from: ‘gdata’
* checking package vignettes ... WARNING
Located more than one ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘user_guide’: ‘user_guide.html’ (3.98423e+06 bytes), ‘user_guide.pdf’ (496045 bytes)
Package vignette without corresponding single PDF/HTML:
  ‘user_guide.Rmd’
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/CrispRVariants.Rcheck/00check.log’
for details.


Installation output

CrispRVariants.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CrispRVariants
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘CrispRVariants’ ...
** using staged installation
** R
** data
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 75 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-seqsToAln.R:98:1'

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
 23.802   0.922  24.715 

Example timings

CrispRVariants.Rcheck/CrispRVariants-Ex.timings

nameusersystemelapsed
CrisprRun-class1.4670.0371.504
CrisprSet-class3.8080.1163.925
abifToFastq000
alleles0.1300.0030.132
alns0.1300.0020.131
barplotAlleleFreqs0.9920.0111.004
consensusSeqs0.3830.0010.384
dispatchDots0.0020.0010.003
findChimeras0.0320.0020.035
getChimeras0.0490.0010.050
indelCounts0.0870.0010.088
intersperse0.0000.0010.001
mergeCrisprSets3.6440.0093.653
mutationEfficiency0.0530.0010.053
narrowAlignments0.2310.0000.231
plotAlignments0.7430.0010.744
plotChimeras1.0430.0031.046
plotFreqHeatmap0.2800.0010.281
plotVariants6.3160.2236.539
readsToTarget3.4950.0253.520
refFromAlns0.3020.0230.325
selectAlnRegionsHelpers0.0010.0000.001
variantCounts0.0490.0020.051