BioC 2.14: CHECK report for SomaticSignatures on morelia

Package: SomaticSignatures

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SomaticSignatures_1.0.1.tar.gz

StartedAt: 2014-10-08 01:41:00 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:46:43 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 342.3 seconds

RetCode: 0

Status:  OK

CheckDir: SomaticSignatures.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SomaticSignatures_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/SomaticSignatures.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SomaticSignatures/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SomaticSignatures’ version ‘1.0.1’
* 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 ‘SomaticSignatures’ can be installed ... [37s/38s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/46s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
kmers 18.581  2.216  22.572
* 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

* installing *source* package ‘SomaticSignatures’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: the specification for S3 class “cluster” in package ‘NMF’ seems equivalent to one from package ‘BiocParallel’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “cluster” in package ‘NMF’ seems equivalent to one from package ‘BiocParallel’: not turning on duplicate class definitions for this class.
* DONE (SomaticSignatures)

name	user	system	elapsed
SomaticSignatures-package	0.013	0.009	0.062
gc	3.484	0.384	3.991
granges-utils	0.444	0.041	0.495
hs-chrs	0.000	0.000	0.001
kmers-data	0.004	0.002	0.007
kmers	18.581	2.216	22.572
mutation-context	2.279	0.322	3.073
mutation-distribution	0.878	0.022	0.901
mutect	0.132	0.001	0.135