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BioC 2.14: CHECK report for sigaR on zin2

This page was generated on 2014-10-08 08:49:22 -0700 (Wed, 08 Oct 2014).

Package 722/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sigaR 1.8.0
Wessel N. van Wieringen
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/sigaR
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: sigaR
Version: 1.8.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.8.0.tar.gz
StartedAt: 2014-10-08 02:48:00 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:52:18 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 257.6 seconds
RetCode: 0
Status:  OK 
CheckDir: sigaR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/sigaR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sigaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sigaR’ version ‘1.8.0’
* 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 ‘sigaR’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘penalized’
A package should be listed in only one of these fields.
* 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
ExpressionSet2weightedSubset: no visible binding for global variable
  ‘sigaR’
RCMestimation : RCMmlH2: multiple local function definitions for
  ‘tau.estimator’ with different formal arguments
RCMtest: no visible binding for global variable ‘sigaR’
RCMtest: no visible binding for global variable ‘quadprog’
RCMtest: no visible binding for global variable ‘MASS’
cghCall2maximumSubset: no visible binding for global variable ‘sigaR’
cghCall2weightedSubset: no visible binding for global variable ‘sigaR’
cghSeg2weightedSubset: no visible binding for global variable ‘sigaR’
entropyTest: no visible binding for global variable ‘sigaR’
entropyTest: no visible binding for global variable ‘corpcor’
matchAnn2Ann: no visible binding for global variable ‘sigaR’
matchCGHcall2ExpressionSet: no visible binding for global variable
  ‘sigaR’
mutInfTest: no visible binding for global variable ‘sigaR’
mutInfTest: no visible binding for global variable ‘corpcor’
* 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 ... [192s/194s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mutInfTest    156.394  3.692 162.367
cisEffectTune  13.973  0.000  14.115
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/sigaR.Rcheck/00check.log’
for details.

sigaR.Rcheck/00install.out:

* installing *source* package ‘sigaR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sigaR)

sigaR.Rcheck/sigaR-Ex.timings:

nameusersystemelapsed
CNGEheatmaps0.9800.0120.991
ExpressionSet2order0.0120.0000.012
ExpressionSet2subset0.0080.0000.009
ExpressionSet2weightedSubset0.1880.0040.190
RCMestimation1.0640.0041.070
RCMrandom1.0240.0001.069
RCMtest3.7400.0003.762
cghCall2cghSeg0.0560.0000.056
cghCall2maximumSubset0.2880.0000.291
cghCall2order0.0160.0000.016
cghCall2subset0.0520.0000.049
cghCall2weightedSubset0.2760.0000.277
cghSeg2order0.0560.0000.055
cghSeg2subset0.0880.0000.089
cghSeg2weightedSubset0.2200.0000.219
cisEffectPlot0.0800.0000.079
cisEffectTable1.5000.0001.513
cisEffectTest1.5560.0001.562
cisEffectTune13.973 0.00014.115
cisTest-class0.0000.0000.001
entTest-class0.0000.0000.001
entropyTest0.1400.0000.141
expandMatching2singleIDs0.0360.0000.035
getSegFeatures0.0000.0080.008
hdEntropy0.0160.0000.014
hdMI0.2680.0000.267
matchAnn2Ann0.0280.0000.031
matchCGHcall2ExpressionSet0.0440.0000.048
merge2ExpressionSets0.0560.0000.059
merge2cghCalls0.0760.0000.078
miTest-class0.0040.0000.001
mutInfTest156.394 3.692162.367
nBreakpoints0.2160.0000.215
pathway1sample0.1200.0040.125
pathway2sample2.7480.2242.986
pathwayFit-class0.0000.0000.001
pathwayPlot0.1080.0080.167
pollackCN160.0040.0000.005
pollackGE160.0000.0000.003
profilesPlot0.1280.0080.138
rcmFit-class0.0040.0000.001
rcmTest-class0.0000.0000.001
splitMatchingAtBreakpoints0.2400.0000.242
uniqGenomicInfo0.0080.0000.007