BioC 3.0: CHECK report for HiTC on oaxaca

Package: HiTC

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HiTC_1.10.0.tar.gz

StartedAt: 2015-04-10 00:29:07 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:34:46 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 339.3 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 --no-multiarch HiTC_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/HiTC.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.10.0’
* 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 ‘HiTC’ can be installed ... [28s/30s] 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
HTCexp: no visible global function definition for ‘seqlevels’
HTClist : <anonymous>: no visible global function definition for
  ‘seqlevels’
binningC: no visible global function definition for ‘seqlevels’
export.my5C : <anonymous>: no visible global function definition for
  ‘seqlevels’
exportC : <anonymous>: no visible global function definition for
  ‘seqlevels’
getAnnotatedRestrictionSites: no visible global function definition for
  ‘seqlevels’
getAnnotatedRestrictionSites: no visible global function definition for
  ‘mclapply’
getBlocsIndex: no visible global function definition for ‘Rle’
getExpectedCounts: no visible global function definition for ‘mclapply’
getRestrictionFragmentsPerChromosome: no visible global function
  definition for ‘seqlevels’
getRestrictionFragmentsPerChromosome: no visible global function
  definition for ‘mclapply’
getRestrictionFragmentsPerChromosome : <anonymous>: no visible global
  function definition for ‘seqlengths’
normLGF: no visible global function definition for ‘seqlevels’
normLGF: no visible global function definition for ‘glm.nb’
setEnvDisplay: no visible global function definition for ‘seqlevels’
setGenomicFeatures: no visible global function definition for
  ‘seqlevels’
slidingWindow: no visible binding for global variable ‘consV’
splitCombinedContacts: no visible global function definition for
  ‘sortSeqlevels’
splitCombinedContacts: no visible global function definition for
  ‘seqlevels’
splitCombinedContacts: no visible global function definition for
  ‘mclapply’
splitCombinedContacts : <anonymous>: no visible global function
  definition for ‘seqlevels<-’
forcePairwise,HTClist: no visible global function definition for
  ‘seqlevels’
forcePairwise,HTClist: no visible global function definition for
  ‘mclapply’
forceSymmetric,HTClist-character: no visible global function definition
  for ‘sortSeqlevels’
forceSymmetric,HTClist-character: no visible global function definition
  for ‘seqlevels’
getCombinedContacts,HTClist: no visible global function definition for
  ‘seqlevels’
isBinned,HTCexp: no visible global function definition for
  ‘countMatches’
isComplete,HTClist: no visible global function definition for
  ‘seqlevels’
isIntraChrom,HTCexp: no visible global function definition for
  ‘seqlevels’
isPairwise,HTClist: no visible global function definition for
  ‘seqlevels’
seqlevels,HTCexp: no visible global function definition for ‘seqlevels’
seqlevels,HTClist: no visible binding for global variable ‘seqlevels’
show,HTCexp: no visible global function definition for ‘seqlevels’
* 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 ... [49s/50s] OK
Examples with CPU or elapsed time > 5s
      user system elapsed
CQC  7.490  0.144   8.108
mapC 6.739  0.312   7.134
* 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/HiTC.Rcheck/00check.log’
for details.

* installing *source* package ‘HiTC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘isSymmetric’ from package ‘base’ in package ‘HiTC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HiTC)

name	user	system	elapsed
CQC	7.490	0.144	8.108
HTCexp-class	4.538	0.198	4.862
HTClist-class	2.759	0.444	3.273
Nora_5C	0.335	0.006	0.343
binningC	2.735	0.098	2.865
discretize	0.001	0.000	0.001
export.my5C	0.001	0.001	0.001
exportC	0.001	0.000	0.001
extractRegion	0.635	0.008	0.653
getAnnotatedRestrictionSites	0.000	0.001	0.001
getExpectedCounts	3.129	0.288	3.357
getRestrictionFragmentsPerChromosome	0.001	0.000	0.001
import.my5C	0.203	0.004	0.208
importC	0.001	0.000	0.001
intervalsDist	0.756	0.029	0.807
mapC	6.739	0.312	7.134
normICE	0.000	0.000	0.001
normLGF	0.001	0.000	0.001
pca.hic	1.585	0.430	1.725
removeIntervals	0.402	0.015	0.424
setGenomicFeatures	0.001	0.001	0.001
setIntervalScale	1.719	0.030	1.760