BioC 3.5: CHECK report for GOTHiC on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOTHiC_1.11.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GOTHiC.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOTHiC/DESCRIPTION’ ... OK
* this is package ‘GOTHiC’ version ‘1.11.1’
* 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 ‘GOTHiC’ can be installed ... 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 ... NOTE
':::' call which should be '::': ‘S4Vectors:::orderIntegerPairs’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.binInteractions: no visible binding for global variable ‘chr1’
.binInteractions: no visible binding for global variable ‘chr2’
.binInteractions: no visible binding for global variable ‘locus1’
.binInteractions: no visible binding for global variable ‘locus2’
.binomialHiC: no visible binding for global variable ‘resGR’
.binomialHiC : <anonymous>: no visible binding for global variable
  ‘frequencies’
.binomialHiC : <anonymous>: no visible binding for global variable
  ‘int1’
.binomialHiC : <anonymous>: no visible binding for global variable
  ‘int2’
.binomialHiC: no visible binding for global variable ‘V1’
.binomialHiC: no visible binding for global variable ‘int1’
.binomialHiC: no visible binding for global variable ‘int2’
.binomialHiC: no visible binding for global variable ‘frequencies’
.binomialHiC : <anonymous>: no visible global function definition for
  ‘binom.test’
.binomialHiC: no visible global function definition for ‘p.adjust’
.binomialHiC: no visible binding for global variable ‘pvalue’
.binomialHiC: no visible global function definition for ‘x11’
.binomialHiC : <anonymous>: no visible global function definition for
  ‘pdf’
.binomialHiC : <anonymous>: no visible global function definition for
  ‘dev.off’
.binomialHiChicup : <anonymous>: no visible binding for global variable
  ‘frequencies’
.binomialHiChicup : <anonymous>: no visible binding for global variable
  ‘int1’
.binomialHiChicup : <anonymous>: no visible binding for global variable
  ‘int2’
.binomialHiChicup: no visible binding for global variable ‘V1’
.binomialHiChicup: no visible binding for global variable ‘int1’
.binomialHiChicup: no visible binding for global variable ‘int2’
.binomialHiChicup: no visible binding for global variable ‘frequencies’
.binomialHiChicup : <anonymous>: no visible global function definition
  for ‘binom.test’
.binomialHiChicup: no visible global function definition for ‘p.adjust’
.binomialHiChicup: no visible binding for global variable ‘pvalue’
.binomialHiChicup: no visible global function definition for ‘x11’
.binomialHiChicup : <anonymous>: no visible global function definition
  for ‘pdf’
.binomialHiChicup : <anonymous>: no visible global function definition
  for ‘dev.off’
.findOverlaps.circle: no visible global function definition for
  ‘IntervalTree’
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for ‘isCircular’
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for ‘seqlengths’
.getHindIIIsitesFromHicup: no visible global function definition for
  ‘read.table’
.getRestrictionSitesFromBSgenome: no visible global function definition
  for ‘biocLite’
.getRestrictionSitesFromBSgenome: no visible global function definition
  for ‘seqlengths’
.importHicup: no visible global function definition for ‘read.table’
.onlyPairing: no visible global function definition for ‘read.table’
.onlyPairing: no visible global function definition for ‘ScanBamParam’
GOTHiC: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19’
GOTHiC: no visible binding for global variable ‘filtered’
GOTHiC: no visible binding for global variable ‘interactingLoci’
mapReadsToRestrictionSites: no visible binding for global variable
  ‘resGR’
Undefined global functions or variables:
  BSgenome.Hsapiens.UCSC.hg19 IntervalTree ScanBamParam V1 binom.test
  biocLite chr1 chr2 dev.off filtered frequencies int1 int2
  interactingLoci isCircular locus1 locus2 p.adjust pdf pvalue
  read.table resGR seqlengths x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "x11")
  importFrom("stats", "binom.test", "p.adjust")
  importFrom("utils", "read.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 ... ERROR
Running examples in ‘GOTHiC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GOTHiChicup
> ### Title: Genome Organisation Through HiC from HiCUP output
> ### Aliases: GOTHiChicup
> ### Keywords: manip package
> 
> ### ** Examples
> 
> library(GOTHiC)
> dirPath <- system.file("extdata", package="HiCDataLymphoblast")
> fileName <- list.files(dirPath, full.names=TRUE)[4]
> restrictionFile <- list.files(dirPath, full.names=TRUE)[3]
> binom=GOTHiChicup(fileName, sampleName='lymphoid_chr20', res=1000000, 
+ restrictionFile, cistrans='all', parallel=FALSE, cores=NULL)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘seqnames’ for signature ‘"integer"’
Calls: GOTHiChicup ... standardGeneric -> eval -> eval -> eval -> seqnames -> <Anonymous>
Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/GOTHiC.Rcheck/00check.log’
for details.
name	user	system	elapsed
GOTHiC	44.508	2.487	51.328
BioC 3.5: CHECK report for GOTHiC on oaxaca

Summary

Command output
