BioC 3.2: CHECK report for SomaticSignatures on perceval

Package: SomaticSignatures

Version: 2.5.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SomaticSignatures_2.5.6.tar.gz

StartedAt: 2015-08-24 05:24:58 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 05:31:55 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 416.5 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 SomaticSignatures_2.5.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SomaticSignatures.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.5.6’
* 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 ... [46s/46s] 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/44s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
number-signatures 19.031  0.033  19.114
* 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

* 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	0.008	0.009	0.035
gc	0.646	0.011	0.658
granges-utils	0.108	0.007	0.115
hs-chrs	0.001	0.000	0.001
kmers-data	0.005	0.005	0.010
kmers	1.353	0.036	1.893
motif-functions	0	0	0
mutation-context	0.271	0.002	0.273
mutation-distribution	0.521	0.007	0.531
mutational-signatures	1.691	0.006	1.699
mutect	0.084	0.001	0.086
number-signatures	19.031	0.033	19.114
sca-data	0.005	0.002	0.006
signature-plot-functions	1.590	0.075	1.677
signatures21-data	0.004	0.001	0.005