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BioC 3.0: CHECK report for SomaticSignatures on oaxaca

This page was generated on 2015-04-10 10:08:35 -0700 (Fri, 10 Apr 2015).

Package 841/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SomaticSignatures 2.2.3
Julian Gehring
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/SomaticSignatures
Last Changed Rev: 96320 / Revision: 102249
Last Changed Date: 2014-11-01 06:38:39 -0700 (Sat, 01 Nov 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: SomaticSignatures
Version: 2.2.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SomaticSignatures_2.2.3.tar.gz
StartedAt: 2015-04-10 03:32:41 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:39:46 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 424.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SomaticSignatures.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SomaticSignatures_2.2.3.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/SomaticSignatures.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.2.3’
* 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 ... [51s/51s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘proxy::as.matrix’ when loading ‘SomaticSignatures’
See ‘/Users/biocbuild/bbs-3.0-bioc/meat/SomaticSignatures.Rcheck/00install.out’ for details.
* 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 ... NOTE
scaSNVRanges: no visible global function definition for
  ‘scaLoadDatasets’
scaSNVRanges: no visible global function definition for ‘scaMetadata’
* 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 ... [26s/29s] 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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 by ‘proxy::as.matrix’ when loading ‘SomaticSignatures’
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
Warning: replacing previous import by ‘proxy::as.matrix’ when loading ‘SomaticSignatures’
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-package0.0140.0110.094
gc1.0060.0331.363
granges-utils0.1490.0080.157
hs-chrs0.0010.0010.002
kmers-data0.0060.0040.010
kmers1.4100.0283.768
motif-functions0.0010.0000.001
mutation-context0.3350.0010.337
mutation-distribution0.6040.0030.607
mutational-signatures1.6230.0041.652
mutect0.0850.0010.087
sca-data0.0080.0020.010
signature-plot-functions1.7530.0171.812
signatures21-data0.0060.0010.008