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BioC 3.5: CHECK report for SomaticSignatures on oaxaca

This page was generated on 2016-11-16 16:25:58 -0500 (Wed, 16 Nov 2016).

Package 1169/1294HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SomaticSignatures 2.11.0
Julian Gehring
Snapshot Date: 2016-11-15 17:15:24 -0500 (Tue, 15 Nov 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SomaticSignatures
Last Changed Rev: 122712 / Revision: 124030
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / 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: 2.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SomaticSignatures_2.11.0.tar.gz
StartedAt: 2016-11-16 06:48:50 -0800 (Wed, 16 Nov 2016)
EndedAt: 2016-11-16 06:55:06 -0800 (Wed, 16 Nov 2016)
EllapsedTime: 376.1 seconds
RetCode: 0
Status:  OK 
CheckDir: SomaticSignatures.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SomaticSignatures_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SomaticSignatures.Rcheck’
* using R Under development (unstable) (2016-10-21 r71549)
* 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 ‘2.11.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
number-signatures 13.076  0.035  13.121
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SomaticSignatures)

SomaticSignatures.Rcheck/SomaticSignatures-Ex.timings:

nameusersystemelapsed
SomaticSignatures-package0.0100.0060.054
gc0.3720.0340.973
granges-utils0.1270.0130.151
hs-chrs0.0010.0000.001
kmers-data0.0040.0040.007
kmers0.7510.0282.034
motif-functions0.0390.0040.042
mutation-context0.1960.0010.198
mutation-distribution0.4950.0020.551
mutational-signatures1.5540.0051.561
mutect0.0640.0010.064
number-signatures13.076 0.03513.121
sca-data0.0120.0010.014
signature-plot-functions2.2070.0542.297
signatures21-data0.0040.0010.006