BioC 3.0: CHECK report for focalCall on zin1

Package: focalCall

Version: 1.0.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings focalCall_1.0.0.tar.gz

StartedAt: 2015-04-10 00:01:08 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:02:11 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 63.0 seconds

RetCode: 0

Status:  OK

CheckDir: focalCall.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings focalCall_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/focalCall.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘focalCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘focalCall’ version ‘1.0.0’
* 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 ‘focalCall’ can be installed ... [4s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 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 ... OK
* checking R code for possible problems ... NOTE
.match_CNV2CGH: no visible global function definition for ‘bpstart’
.match_CNV2CGH: no visible global function definition for ‘chromosomes’
.match_CNV2CGH: no visible global function definition for ‘bpend’
FreqPlot: no visible global function definition for ‘chromosomes’
FreqPlotfocal: no visible global function definition for ‘chromosomes’
FreqPlotfocal: no visible global function definition for
  ‘assayDataElement’
FreqPlotfocal: no visible global function definition for ‘fData’
focalCall: no visible global function definition for ‘calls’
focalCall: no visible global function definition for ‘featureNames’
focalCall: no visible global function definition for ‘segmented’
focalCall: no visible global function definition for ‘chromosomes’
focalCall: no visible global function definition for ‘bpstart’
focalCall: no visible global function definition for
  ‘assayDataElement<-’
focalCall: no visible global function definition for ‘assayDataElement’
focalCall: no visible global function definition for ‘bpend’
focalCall: no visible global function definition for ‘fData’
focalCall: no visible global function definition for ‘fData<-’
igvFiles: no visible global function definition for ‘calls’
igvFiles: no visible global function definition for ‘chromosomes’
igvFiles: no visible global function definition for ‘bpstart’
igvFiles: no visible global function definition for ‘bpend’
igvFiles: no visible global function definition for ‘featureNames’
igvFiles: no visible global function definition for ‘segmented’
igvFiles: no visible global function definition for ‘assayDataElement’
singleSample: no visible global function definition for ‘calls’
singleSample: no visible global function definition for ‘featureNames’
singleSample: no visible global function definition for ‘fData’
singleSample: no visible global function definition for ‘fData<-’
singleSample: no visible global function definition for
  ‘assayDataElement<-’
singleSample: no visible global function definition for ‘segmented’
singleSample: no visible global function definition for ‘chromosomes’
singleSample: no visible global function definition for ‘bpend’
singleSample: no visible global function definition for ‘bpstart’
singleSample: no visible global function definition for
  ‘assayDataElement’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/15s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
focalCall 5.864  0.048   5.952
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 [2s/2s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/focalCall.Rcheck/00check.log’
for details.

* installing *source* package ‘focalCall’ ...
** 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 (focalCall)

name	user	system	elapsed
BierkensCNA	0.640	0.020	0.661
FreqPlot	0.596	0.004	0.613
FreqPlotfocal	0.624	0.008	0.637
focalCall	5.864	0.048	5.952
igvFiles	1.732	0.016	1.777
singleSample	2.964	0.016	3.111