Helen Lindsay
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CrispRVariants |
| Branch: RELEASE_3_7 |
| Last Commit: c9f0422 |
| Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:55:47 -0400 (Wed, 17 Oct 2018).
| Package 323/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CrispRVariants 1.8.0 Helen Lindsay
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CrispRVariants |
| Version: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2018-10-16 20:43:56 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:48:32 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 276.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CrispRVariants.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CrispRVariants.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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 ... OK
* 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 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 8.494 0.224 8.772
CrisprSet-class 5.476 0.086 5.669
mergeCrisprSets 5.076 0.041 5.144
* 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: OK
CrispRVariants.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CrispRVariants ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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)
CrispRVariants.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 FAILED: 0
>
> proc.time()
user system elapsed
28.148 0.879 29.251
CrispRVariants.Rcheck/CrispRVariants-Ex.timings
| name | user | system | elapsed | |
| CrisprRun-class | 0.763 | 0.058 | 0.836 | |
| CrisprSet-class | 5.476 | 0.086 | 5.669 | |
| abifToFastq | 0.274 | 0.010 | 0.287 | |
| alleles | 0.159 | 0.009 | 0.169 | |
| alns | 0.729 | 0.009 | 0.750 | |
| barplotAlleleFreqs | 1.254 | 0.013 | 1.275 | |
| consensusSeqs | 0.536 | 0.009 | 0.546 | |
| dispatchDots | 0.006 | 0.000 | 0.007 | |
| findChimeras | 0.039 | 0.001 | 0.041 | |
| getChimeras | 0.040 | 0.002 | 0.042 | |
| indelCounts | 0.144 | 0.001 | 0.148 | |
| intersperse | 0.002 | 0.000 | 0.002 | |
| mergeCrisprSets | 5.076 | 0.041 | 5.144 | |
| mutationEfficiency | 0.046 | 0.002 | 0.049 | |
| narrowAlignments | 0.296 | 0.001 | 0.304 | |
| plotAlignments | 0.994 | 0.009 | 1.012 | |
| plotChimeras | 1.374 | 0.005 | 1.392 | |
| plotFreqHeatmap | 0.416 | 0.005 | 0.424 | |
| plotVariants | 8.494 | 0.224 | 8.772 | |
| readsToTarget | 4.478 | 0.046 | 4.567 | |
| selectAlnRegionsHelpers | 0.002 | 0.001 | 0.002 | |
| variantCounts | 0.044 | 0.004 | 0.049 | |