BioC 2.14: CHECK report for GOTHiC on petty

Package: GOTHiC

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GOTHiC_1.1.2.tar.gz

StartedAt: 2014-10-07 22:18:57 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:28:24 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 566.6 seconds

RetCode: 0

Status:  OK

CheckDir: GOTHiC.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 --no-multiarch GOTHiC_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GOTHiC.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOTHiC/DESCRIPTION’ ... OK
* this is package ‘GOTHiC’ version ‘1.1.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’
* 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 ... [46s/46s] 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘IRanges:::orderIntegerPairs’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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: no visible binding for global variable ‘frequencies’
.binomialHiC: no visible binding for global variable ‘int1’
.binomialHiC: no visible binding for global variable ‘int2’
.binomialHiC: no visible binding for global variable ‘pvalue’
.getRestrictionSitesFromBSgenome: no visible global function definition
  for ‘biocLite’
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’
* 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 ... [128s/130s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
GOTHiC    88.217  5.712  95.016
pairReads  8.589  0.546   9.172
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/GOTHiC.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GOTHiC	88.217	5.712	95.016
filtered	0.153	0.014	0.175
mapReadsToRestrictionSites	2.122	0.113	2.298
pairReads	8.589	0.546	9.172