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CHECK report for focalCall on veracruz1

This page was generated on 2018-04-12 13:39:35 -0400 (Thu, 12 Apr 2018).

Package 502/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
focalCall 1.12.0
Oscar Krijgsman
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/focalCall
Branch: RELEASE_3_6
Last Commit: 7ccdb60
Last Changed Date: 2017-10-30 12:40:42 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: focalCall
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings focalCall_1.12.0.tar.gz
StartedAt: 2018-04-12 03:52:47 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:53:43 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 55.1 seconds
RetCode: 0
Status:  OK 
CheckDir: focalCall.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings focalCall_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/focalCall.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 ‘focalCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘focalCall’ version ‘1.12.0’
* 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 ... 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 ... 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’
FreqPlot: no visible global function definition for ‘plot’
FreqPlot: no visible global function definition for ‘points’
FreqPlot: no visible global function definition for ‘abline’
FreqPlot: no visible global function definition for ‘axis’
FreqPlotfocal: no visible global function definition for ‘chromosomes’
FreqPlotfocal: no visible global function definition for
  ‘assayDataElement’
FreqPlotfocal: no visible global function definition for ‘fData’
FreqPlotfocal: no visible global function definition for ‘plot’
FreqPlotfocal: no visible global function definition for ‘points’
FreqPlotfocal: no visible global function definition for ‘abline’
FreqPlotfocal: no visible global function definition for ‘axis’
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<-’
focalCall: no visible global function definition for ‘write.table’
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 ‘write.table’
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’
singleSample: no visible global function definition for ‘median’
singleSample: no visible global function definition for ‘png’
singleSample: no visible global function definition for ‘plot’
singleSample: no visible global function definition for ‘dev.off’
singleSample: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline assayDataElement assayDataElement<- axis bpend bpstart calls
  chromosomes dev.off fData fData<- featureNames median plot png points
  segmented write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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
focalCall 5.173  0.098   5.343
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/focalCall.Rcheck/00check.log’
for details.



Installation output

focalCall.Rcheck/00install.out

* 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)

Tests output

focalCall.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("focalCall")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA


Attaching package: 'snow'

The following objects are masked from 'package:BiocGenerics':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, parApply, parCapply,
    parLapply, parRapply, parSapply

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster


Attaching package: 'CGHcall'

The following object is masked from 'package:BiocGenerics':

    normalize



RUNIT TEST PROTOCOL -- Thu Apr 12 03:53:39 2018 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
focalCall RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.286   0.072   1.357 

Example timings

focalCall.Rcheck/focalCall-Ex.timings

nameusersystemelapsed
BierkensCNA0.5420.0320.590
FreqPlot0.4940.0300.541
FreqPlotfocal0.7080.0300.752
focalCall5.1730.0985.343
igvFiles1.5440.0611.622
singleSample2.4370.0912.584