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BioC 2.13: CHECK report for sigaR on perceval

This page was generated on 2014-04-05 09:52:46 -0700 (Sat, 05 Apr 2014).

Package 656/750HostnameOS / ArchBUILDCHECKBUILD BIN
sigaR 1.6.0
Wessel N. van Wieringen
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/sigaR
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: sigaR
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sigaR_1.6.0.tar.gz
StartedAt: 2014-04-05 04:19:52 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:27:48 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 476.0 seconds
RetCode: 0
Status:  OK 
CheckDir: sigaR.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/sigaR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.6.0’
* 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 ... [9s/10s] 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
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’
ExpressionSet2weightedSubset: no visible binding for global variable
  ‘sigaR’
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’
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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘sigaR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [352s/362s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     271.586 21.828 298.975
cisEffectTune   23.878  0.342  26.511
pathway2sample   7.395  1.425   8.942
RCMtest          5.373  0.024   5.800
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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
CNGEheatmaps1.7550.0541.829
ExpressionSet2order0.0240.0020.025
ExpressionSet2subset0.0230.0010.024
ExpressionSet2weightedSubset0.3130.0130.326
RCMestimation1.3820.0081.412
RCMrandom1.5610.0071.584
RCMtest5.3730.0245.800
cghCall2cghSeg0.0810.0010.090
cghCall2maximumSubset0.5110.0170.591
cghCall2order0.0310.0010.032
cghCall2subset0.0940.0030.108
cghCall2weightedSubset0.4020.0060.435
cghSeg2order0.0900.0020.114
cghSeg2subset0.1420.0020.155
cghSeg2weightedSubset0.3890.0030.420
cisEffectPlot0.1200.0040.135
cisEffectTable2.7600.0923.272
cisEffectTest2.5390.0872.932
cisEffectTune23.878 0.34226.511
cisTest-class0.0100.0000.013
entTest-class0.0110.0010.011
entropyTest0.2980.0040.326
expandMatching2singleIDs0.0940.0070.158
getSegFeatures0.0270.0020.048
hdEntropy0.0320.0010.034
hdMI0.5980.0060.650
matchAnn2Ann0.0700.0040.102
matchCGHcall2ExpressionSet0.0910.0020.101
merge2ExpressionSets0.1120.0020.121
merge2cghCalls0.1380.0050.191
miTest-class0.0090.0010.010
mutInfTest271.586 21.828298.975
nBreakpoints0.3770.0220.402
pathway1sample0.2540.0400.301
pathway2sample7.3951.4258.942
pathwayFit-class0.0030.0040.008
pathwayPlot0.1520.0250.180
pollackCN160.0070.0050.012
pollackGE160.0120.0120.025
profilesPlot0.1860.0120.199
rcmFit-class0.0030.0040.007
rcmTest-class0.0040.0050.010
splitMatchingAtBreakpoints0.3370.0190.360
uniqGenomicInfo0.0120.0070.020