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Package 538/609HostnameOS / ArchBUILDCHECKBUILD BIN
sigaR 1.2.1
Wessel N. van Wieringen
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/sigaR
Last Changed Rev: 73855 / Revision: 74773
Last Changed Date: 2013-03-01 10:54:40 -0800 (Fri, 01 Mar 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: sigaR
Version: 1.2.1
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sigaR_1.2.1.tar.gz
StartedAt: 2013-03-25 01:16:13 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:24:29 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 495.5 seconds
RetCode: 0
Status:  OK 
CheckDir: sigaR.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/sigaR.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'sigaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigaR' version '1.2.1'
* 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 whether package 'sigaR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     225.153 80.917 338.944
cisEffectTune   20.971  0.180  22.433
pathway2sample   5.679  2.785   8.986
RCMtest          5.419  0.017   5.678
* 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
  '/Users/biocbuild/bbs-2.11-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
CNGEheatmaps1.3920.0651.685
ExpressionSet2order0.0150.0040.019
ExpressionSet2subset0.0110.0010.012
ExpressionSet2weightedSubset0.2410.0070.294
RCMestimation1.4780.0151.564
RCMrandom1.3780.0071.406
RCMtest5.4190.0175.678
cghCall2cghSeg0.0720.0030.075
cghCall2maximumSubset0.4250.0170.454
cghCall2order0.0230.0040.027
cghCall2subset0.0700.0030.074
cghCall2weightedSubset0.3050.0120.319
cghSeg2order0.0690.0040.073
cghSeg2subset0.1100.0030.114
cghSeg2weightedSubset0.2760.0080.287
cisEffectPlot0.0950.0050.101
cisEffectTable2.6820.0572.814
cisEffectTest2.6850.0592.993
cisEffectTune20.971 0.18022.433
cisTest-class0.0010.0000.002
entTest-class0.0010.0000.001
entropyTest0.1950.0090.247
expandMatching2singleIDs0.0610.0020.063
getSegFeatures0.0100.0020.016
hdEntropy0.0170.0030.025
hdMI0.3920.0060.409
matchAnn2Ann0.0580.0030.066
matchCGHcall2ExpressionSet0.0790.0050.099
merge2ExpressionSets0.0840.0020.092
merge2cghCalls0.1310.0080.160
miTest-class0.0000.0000.001
mutInfTest225.153 80.917338.944
nBreakpoints0.3110.0080.320
pathway1sample0.2060.0490.261
pathway2sample5.6792.7858.986
pathwayFit-class0.0010.0000.001
pathwayPlot0.1720.0550.246
pollackCN160.0060.0010.007
pollackGE160.0030.0010.004
profilesPlot0.1780.0120.198
rcmFit-class0.0010.0010.001
rcmTest-class0.0010.0000.001
splitMatchingAtBreakpoints0.3190.0040.324
uniqGenomicInfo0.0100.0010.011