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Package 107/554HostnameOS / ArchBUILDCHECKBUILD BIN
Clonality 1.4.0
Irina Ostrovnaya
Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/Clonality
Last Changed Rev: 64678 / Revision: 64719
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
puck5 Linux (Ubuntu 12.04) / 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: Clonality
Version: 1.4.0
Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings Clonality_1.4.0.tar.gz
StartedAt: 2012-04-01 00:20:01 -0700 (Sun, 01 Apr 2012)
EndedAt: 2012-04-01 00:21:47 -0700 (Sun, 01 Apr 2012)
EllapsedTime: 105.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Clonality.Rcheck
Warnings: 0

Command output

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Clonality.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Clonality/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clonality' version '1.4.0'
* 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 whether package 'Clonality' 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 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
ave.adj.probes: warning in CNA(as.matrix(all.ave[, -1]), chrom = chrs,
  maploc = as.numeric(all.ave[, 1]), sample = names(data)[-c(1, 2)]):
  partial argument match of 'sample' to 'sampleid'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Clonality.Rcheck/00check.log'
for details.

Clonality.Rcheck/00install.out:

* installing *source* package 'Clonality' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'Clonality.Rnw' 
** testing if installed package can be loaded

* DONE (Clonality)

Clonality.Rcheck/Clonality-Ex.timings:

nameusersystemelapsed
LOHclonality28.717 0.00828.741
ave.adj.probes000
chromosomePlots000
clonality.analysis55.707 0.34860.244
genomewidePlots0.0000.0000.001
histogramPlot0.0040.0000.001
splitChromosomes000