BioC 3.6: CHECK report for SeqVarTools on veracruz1
This page was generated on 2017-08-16 13:44:17 -0400 (Wed, 16 Aug 2017).
SeqVarTools 1.15.1 Stephanie M. Gogarten
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SeqVarTools | Last Changed Rev: 129656 / Revision: 131943 | Last Changed Date: 2017-05-17 12:46:54 -0400 (Wed, 17 May 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
Summary
Package: SeqVarTools |
Version: 1.15.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqVarTools_1.15.1.tar.gz |
StartedAt: 2017-08-16 08:27:58 -0400 (Wed, 16 Aug 2017) |
EndedAt: 2017-08-16 08:31:04 -0400 (Wed, 16 Aug 2017) |
EllapsedTime: 185.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SeqVarTools.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqVarTools_1.15.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SeqVarTools.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqVarTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqVarTools’ version ‘1.15.1’
* 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 ‘SeqVarTools’ 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.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
SeqVarTools.Rcheck/00install.out:
* installing *source* package ‘SeqVarTools’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SeqVarTools)
SeqVarTools.Rcheck/SeqVarTools-Ex.timings:
name | user | system | elapsed
|
SeqVarData-class | 0.133 | 0.010 | 0.157 |
|
allele-methods | 0.052 | 0.009 | 0.060 |
|
alleleFrequency | 0.146 | 0.015 | 0.162 |
|
alternateAlleleDetection | 0.001 | 0.000 | 0.001 |
|
applyMethod | 0.776 | 0.016 | 0.812 |
|
countSingletons | 0.084 | 0.002 | 0.089 |
|
duplicateDiscordance | 0.099 | 0.003 | 0.104 |
|
getGenotype | 0.044 | 0.003 | 0.049 |
|
getVariableLengthData | 0.033 | 0.002 | 0.039 |
|
heterozygosity | 0.227 | 0.024 | 0.263 |
|
hwe | 0.091 | 0.010 | 0.101 |
|
inbreedCoeff | 0.222 | 0.014 | 0.240 |
|
isSNV | 0.003 | 0.000 | 0.004 |
|
isVariant | 0.005 | 0.001 | 0.006 |
|
meanBySample | 0.040 | 0.003 | 0.043 |
|
mendelErr | 0.036 | 0.002 | 0.039 |
|
missingGenotypeRate | 0.035 | 0.004 | 0.039 |
|
pca | 0.374 | 0.063 | 0.451 |
|
pedigree | 0.006 | 0.001 | 0.007 |
|
refFrac | 0.082 | 0.003 | 0.087 |
|
regression | 0.110 | 0.004 | 0.114 |
|
setVariantID | 0.009 | 0.003 | 0.012 |
|
titv | 0.259 | 0.007 | 0.280 |
|