Package: Clonality

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Clonality_1.26.0.tar.gz

StartedAt: 2018-04-12 01:49:15 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:52:20 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 184.3 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_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Clonality.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.26.0’
* 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 ... 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.
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
clonality.analysis  68.233  0.369  69.844
LRtesting3or4tumors 60.634  0.109  61.959
LOHclonality         8.867  0.232   9.261
ECMtesting           7.987  0.031   8.178
* 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-3.6-bioc/meat/Clonality.Rcheck/00check.log’
for details.

* installing *source* package ‘Clonality’ ...
** R
** data
** 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	7.987	0.031	8.178
LOHclonality	8.867	0.232	9.261
LRtesting3or4tumors	60.634	0.109	61.959
SNVtest	0.452	0.020	0.496
ave.adj.probes	1.322	0.035	1.388
chromosomePlots	0	0	0
clonality.analysis	68.233	0.369	69.844
genomewidePlots	0.001	0.001	0.000
histogramPlot	0.000	0.000	0.001
mutation.proba	0.910	0.010	0.938
mutation.rem	2.786	0.028	2.871
splitChromosomes	0.042	0.001	0.043