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Package 557/631HostnameOS / ArchBUILDCHECKBUILD BIN
sigaR 1.3.1
Wessel N. van Wieringen
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sigaR
Last Changed Rev: 72298 / Revision: 72575
Last Changed Date: 2013-01-04 13:18:09 -0800 (Fri, 04 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: sigaR
Version: 1.3.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.3.1.tar.gz
StartedAt: 2013-01-16 06:19:11 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 06:25:47 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 396.5 seconds
RetCode: 0
Status:  OK 
CheckDir: sigaR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/sigaR.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.3.1’
* 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 ... OK
* checking installed package size ... OK
* checking package 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 for unstated 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 examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     245.324  7.176 256.295
cisEffectTune   21.841  0.004  21.849
pathway2sample   6.188  0.452   6.643
RCMtest          5.408  0.004   5.413
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-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
   ‘sigaR.Rnw’ 
** testing if installed package can be loaded

* DONE (sigaR)

sigaR.Rcheck/sigaR-Ex.timings:

nameusersystemelapsed
CNGEheatmaps1.4720.0241.499
ExpressionSet2order0.0240.0000.025
ExpressionSet2subset0.1480.0000.147
ExpressionSet2weightedSubset0.3040.0040.312
RCMestimation1.3840.0041.394
RCMrandom1.4160.0001.417
RCMtest5.4080.0045.413
cghCall2cghSeg0.0880.0040.092
cghCall2maximumSubset0.5160.0080.526
cghCall2order0.0360.0000.037
cghCall2subset0.0760.0000.074
cghCall2weightedSubset0.3600.0000.367
cghSeg2order0.0920.0000.092
cghSeg2subset0.2520.0000.256
cghSeg2weightedSubset0.3320.0000.335
cisEffectPlot0.1080.0000.106
cisEffectTable2.4450.0002.444
cisEffectTest2.4280.0042.436
cisEffectTune21.841 0.00421.849
cisTest-class0.0080.0040.012
entTest-class0.0120.0000.012
entropyTest0.3000.0080.305
expandMatching2singleIDs0.0680.0080.078
getSegFeatures0.1560.0040.159
hdEntropy0.0240.0000.022
hdMI0.5000.0040.505
matchAnn2Ann0.0720.0000.069
matchCGHcall2ExpressionSet0.0800.0000.084
merge2ExpressionSets0.0920.0000.092
merge2cghCalls0.1200.0040.126
miTest-class0.0120.0000.012
mutInfTest245.324 7.176256.295
nBreakpoints0.3120.0160.326
pathway1sample0.2280.0040.231
pathway2sample6.1880.4526.643
pathwayFit-class0.0040.0000.004
pathwayPlot0.1880.0000.189
pollackCN160.0040.0040.008
pollackGE160.0080.0000.007
profilesPlot0.1640.0040.169
rcmFit-class0.0080.0000.004
rcmTest-class0.0000.0040.004
splitMatchingAtBreakpoints0.3240.0040.331
uniqGenomicInfo0.0120.0000.015