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BioC 3.2: CHECK report for SomaticSignatures on oaxaca

This page was generated on 2016-04-23 10:27:32 -0700 (Sat, 23 Apr 2016).

Package 998/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SomaticSignatures 2.6.1
Julian Gehring
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/SomaticSignatures
Last Changed Rev: 116064 / Revision: 116712
Last Changed Date: 2016-04-10 02:13:40 -0700 (Sun, 10 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SomaticSignatures
Version: 2.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SomaticSignatures_2.6.1.tar.gz
StartedAt: 2016-04-23 04:37:37 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:43:57 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 380.0 seconds
RetCode: 0
Status:  OK 
CheckDir: SomaticSignatures.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 SomaticSignatures_2.6.1.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SomaticSignatures.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘2.6.1’
* 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 ... [44s/49s] OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
* 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 ... [36s/41s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
number-signatures 12.253  0.028  12.312
* 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-3.2-bioc/meat/SomaticSignatures.Rcheck/00check.log’
for details.


SomaticSignatures.Rcheck/00install.out:

* installing *source* package ‘SomaticSignatures’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
* DONE (SomaticSignatures)

SomaticSignatures.Rcheck/SomaticSignatures-Ex.timings:

nameusersystemelapsed
SomaticSignatures-package0.0100.0080.135
gc0.5510.0131.340
granges-utils0.1180.0060.244
hs-chrs0.0010.0010.001
kmers-data0.0050.0010.006
kmers1.1660.0204.511
motif-functions0.0010.0000.001
mutation-context0.3460.0020.348
mutation-distribution0.5180.0030.560
mutational-signatures1.5400.0041.632
mutect0.0890.0010.090
number-signatures12.253 0.02812.312
sca-data0.0060.0010.006
signature-plot-functions2.2070.0492.822
signatures21-data0.0030.0000.004