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BioC 3.4: CHECK report for CrispRVariants on morelia

This page was generated on 2016-09-21 03:55:27 -0700 (Wed, 21 Sep 2016).

Package 271/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CrispRVariants 1.1.4
Helen Lindsay
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CrispRVariants
Last Changed Rev: 118904 / Revision: 121152
Last Changed Date: 2016-06-23 07:11:22 -0700 (Thu, 23 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CrispRVariants
Version: 1.1.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CrispRVariants_1.1.4.tar.gz
StartedAt: 2016-09-20 05:10:28 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:13:39 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 191.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CrispRVariants.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CrispRVariants_1.1.4.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CrispRVariants.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.4’
* 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 loading without being on the library search path ... 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 ‘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:

* installing *source* package ‘CrispRVariants’ ...
** 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 (CrispRVariants)

CrispRVariants.Rcheck/CrispRVariants-Ex.timings:

nameusersystemelapsed
CrisprRun-class0.4970.0300.528
CrisprSet-class3.2080.0593.267
abifToFastq0.1740.0040.179
barplotAlleleFreqs0.5280.0030.532
consensusSeqs0.3860.0030.390
dispatchDots0.0010.0000.002
findChimeras0.0350.0060.041
getChimeras0.0320.0010.033
indelCounts0.0720.0040.076
mergeCrisprSets3.3630.0663.430
mutationEfficiency0.0200.0010.021
narrowAlignments0.2330.0040.236
plotAlignments0.6170.0090.626
plotChimeras0.8420.0070.850
plotFreqHeatmap0.2700.0020.272
plotVariants4.7680.0794.851
readsToTarget3.2900.0493.339
variantCounts0.0230.0020.025