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BioC 3.2: CHECK report for SomaticSignatures on zin1

This page was generated on 2015-08-24 10:49:45 -0700 (Mon, 24 Aug 2015).

Package 967/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SomaticSignatures 2.5.6
Julian Gehring
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SomaticSignatures
Last Changed Rev: 106993 / Revision: 107696
Last Changed Date: 2015-08-03 02:30:58 -0700 (Mon, 03 Aug 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: 2.5.6
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SomaticSignatures_2.5.6.tar.gz
StartedAt: 2015-08-24 03:57:23 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 04:01:51 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 268.4 seconds
RetCode: 0
Status:  OK 
CheckDir: SomaticSignatures.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SomaticSignatures_2.5.6.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SomaticSignatures.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [30s/30s] 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 ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
number-signatures 10.216  0.004  10.236
* 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

SomaticSignatures.Rcheck/00install.out:

* 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)

SomaticSignatures.Rcheck/SomaticSignatures-Ex.timings:

nameusersystemelapsed
SomaticSignatures-package0.0030.0180.024
gc0.4380.0040.453
granges-utils0.0990.0000.099
hs-chrs0.0010.0000.001
kmers-data0.0040.0000.005
kmers0.9420.0081.093
motif-functions0.0010.0000.001
mutation-context0.1980.0000.198
mutation-distribution0.4090.0000.408
mutational-signatures1.1900.0281.228
mutect0.0620.0000.063
number-signatures10.216 0.00410.236
sca-data0.0040.0000.004
signature-plot-functions1.2840.0441.351
signatures21-data0.0020.0040.005