BioC 3.1: CHECK report for SomaticSignatures on morelia

Package: SomaticSignatures

Version: 2.4.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SomaticSignatures_2.4.8.tar.gz

StartedAt: 2015-10-09 06:31:51 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:36:42 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 290.3 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 SomaticSignatures_2.4.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/SomaticSignatures.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.4.8’
* 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 ... [35s/36s] OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
* 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 ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
number-signatures 9.273  0.245   9.521
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/SomaticSignatures.Rcheck/00check.log’
for details.

* installing *source* package ‘SomaticSignatures’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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	0.012	0.012	0.046
gc	0.778	0.099	0.892
granges-utils	0.088	0.012	0.100
hs-chrs	0.001	0.000	0.002
kmers-data	0.004	0.004	0.008
kmers	1.016	0.020	1.036
motif-functions	0	0	0
mutation-context	0.185	0.000	0.185
mutation-distribution	0.417	0.013	0.445
mutational-signatures	1.162	0.048	1.244
mutect	0.052	0.000	0.053
number-signatures	9.273	0.245	9.521
sca-data	0.005	0.001	0.006
signature-plot-functions	1.538	0.098	1.637
signatures21-data	0.003	0.000	0.004