BioC 3.2: CHECK report for Clonality on perceval

Package: Clonality

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Clonality_1.18.0.tar.gz

StartedAt: 2015-11-10 03:20:59 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 03:25:05 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 246.4 seconds

RetCode: 0

Status:  OK

CheckDir: Clonality.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Clonality_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Clonality.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Clonality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Clonality’ version ‘1.18.0’
* 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 ‘Clonality’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘DNAcopy’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [219s/219s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
clonality.analysis  97.232  0.542  97.872
LRtesting3or4tumors 83.468  0.051  83.522
LOHclonality        19.577  0.395  19.972
ECMtesting          14.987  0.011  14.999
* 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/Clonality.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
ECMtesting	14.987	0.011	14.999
LOHclonality	19.577	0.395	19.972
LRtesting3or4tumors	83.468	0.051	83.522
ave.adj.probes	1.772	0.041	1.813
chromosomePlots	0	0	0
clonality.analysis	97.232	0.542	97.872
genomewidePlots	0.000	0.000	0.001
histogramPlot	0.000	0.000	0.001
splitChromosomes	0.012	0.001	0.012