BioC 3.3: CHECK report for Clonality on morelia

Package: Clonality

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Clonality_1.19.0.tar.gz

StartedAt: 2015-10-22 04:36:43 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 04:39:26 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 163.2 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_1.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Clonality.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.19.0’
* 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 ... [138s/138s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
clonality.analysis  64.841  0.342  65.264
LRtesting3or4tumors 49.948  0.053  50.010
LOHclonality        11.711  0.264  11.986
ECMtesting           9.103  0.015   9.121
* 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-3.3-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	9.103	0.015	9.121
LOHclonality	11.711	0.264	11.986
LRtesting3or4tumors	49.948	0.053	50.010
ave.adj.probes	1.158	0.031	1.189
chromosomePlots	0	0	0
clonality.analysis	64.841	0.342	65.264
genomewidePlots	0	0	0
histogramPlot	0.001	0.000	0.000
splitChromosomes	0.009	0.001	0.008