BioC 3.5: CHECK report for HiTC on toluca2

Package: HiTC

Version: 1.19.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HiTC_1.19.1.tar.gz

StartedAt: 2017-04-23 05:17:19 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:22:25 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 305.9 seconds

RetCode: 0

Status:  OK

CheckDir: HiTC.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 HiTC_1.19.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/HiTC.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.19.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HiTC’ 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 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
directionalityIndex: no visible global function definition for
  ‘subjectHits’
directionalityIndex: no visible global function definition for
  ‘queryHits’
getBlocsIndex: no visible global function definition for ‘Rle’
getExpectedCountsMean: no visible global function definition for ‘Rle’
normLGF: no visible global function definition for ‘glm.nb’
slidingWindow: no visible binding for global variable ‘consV’
splitCombinedContacts : <anonymous>: no visible global function
  definition for ‘seqlevels<-’
divide,HTCexp-HTCexp: no visible global function definition for
  ‘queryHits’
divide,HTCexp-HTCexp: no visible global function definition for
  ‘subjectHits’
isBinned,HTCexp: no visible global function definition for
  ‘countMatches’
substract,HTCexp-HTCexp: no visible global function definition for
  ‘queryHits’
substract,HTCexp-HTCexp: no visible global function definition for
  ‘subjectHits’
Undefined global functions or variables:
  Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits
* 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
directionalityIndex 54.884  0.693  56.249
HTCexp-class         5.870  0.207   6.141
mapC                 4.583  0.379   5.537
* 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-3.5-bioc/meat/HiTC.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
CQC	3.797	0.253	4.086
HTCexp-class	5.870	0.207	6.141
HTClist-class	1.326	0.012	1.348
Nora_5C	0.271	0.002	0.274
binningC	1.336	0.012	1.356
directionalityIndex	54.884	0.693	56.249
discretize	0.000	0.000	0.001
export.my5C	0.001	0.000	0.002
exportC	0.001	0.000	0.000
extractRegion	0.584	0.006	0.621
getAnnotatedRestrictionSites	0.001	0.000	0.001
getExpectedCounts	2.561	0.597	3.378
getPearsonMap	0.941	0.058	1.151
getRestrictionFragmentsPerChromosome	0.001	0.000	0.001
import.my5C	0.098	0.001	0.117
importC	0.001	0.001	0.001
intervalsDist	0.453	0.012	0.539
mapC	4.583	0.379	5.537
normICE	0.001	0.000	0.002
normLGF	0.002	0.000	0.001
pca.hic	0.820	0.011	0.953
removeIntervals	0.356	0.004	0.413
setGenomicFeatures	0.001	0.001	0.002
setIntervalScale	1.028	0.009	1.181