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BioC 3.0: CHECK report for HiTC on oaxaca

This page was generated on 2015-04-10 10:05:59 -0700 (Fri, 10 Apr 2015).

Package 428/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiTC 1.10.0
Nicolas Servant
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/HiTC
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

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

Command output

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


* 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.

HiTC.Rcheck/00install.out:

* 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)

HiTC.Rcheck/HiTC-Ex.timings:

nameusersystemelapsed
CQC7.4900.1448.108
HTCexp-class4.5380.1984.862
HTClist-class2.7590.4443.273
Nora_5C0.3350.0060.343
binningC2.7350.0982.865
discretize0.0010.0000.001
export.my5C0.0010.0010.001
exportC0.0010.0000.001
extractRegion0.6350.0080.653
getAnnotatedRestrictionSites0.0000.0010.001
getExpectedCounts3.1290.2883.357
getRestrictionFragmentsPerChromosome0.0010.0000.001
import.my5C0.2030.0040.208
importC0.0010.0000.001
intervalsDist0.7560.0290.807
mapC6.7390.3127.134
normICE0.0000.0000.001
normLGF0.0010.0000.001
pca.hic1.5850.4301.725
removeIntervals0.4020.0150.424
setGenomicFeatures0.0010.0010.001
setIntervalScale1.7190.0301.760