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BioC 3.0: CHECK report for hiAnnotator on zin1

This page was generated on 2015-04-10 09:42:03 -0700 (Fri, 10 Apr 2015).

Package 424/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiAnnotator 1.0.0
Nirav V Malani
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/hiAnnotator
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  OK  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: hiAnnotator
Version: 1.0.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings hiAnnotator_1.0.0.tar.gz
StartedAt: 2015-04-10 01:01:25 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:05:18 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 233.0 seconds
RetCode: 0
Status:  OK 
CheckDir: hiAnnotator.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings hiAnnotator_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/hiAnnotator.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiAnnotator/DESCRIPTION’ ... OK
* this is package ‘hiAnnotator’ version ‘1.0.0’
* 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 ‘hiAnnotator’ can be installed ... [20s/20s] 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
get2NearestFeature: no visible global function definition for ‘IRanges’
get2NearestFeature: no visible global function definition for ‘mid’
getFeatureCounts : <anonymous>: no visible global function definition
  for ‘countQueryHits’
getFeatureCountsBig: no visible global function definition for ‘mid’
getNearestFeature: no visible global function definition for ‘IRanges’
getNearestFeature: no visible global function definition for ‘mid’
makeChunks: no visible global function definition for ‘breakInChunks’
makeChunks: no visible global function definition for ‘detectCores’
makeChunks : <anonymous>: no visible global function definition for
  ‘keepSeqlevels’
makeChunks : <anonymous>: no visible global function definition for
  ‘seqlevels’
makeGRanges: no visible global function definition for ‘IRanges’
makeGRanges: no visible global function definition for ‘seqlengths’
makeGRanges: no visible global function definition for ‘seqlevels<-’
makeGRanges: no visible global function definition for ‘sortSeqlevels’
makeGRanges: no visible global function definition for ‘seqlevels’
makeGRanges: no visible global function definition for ‘seqlengths<-’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
get2NearestFeature 6.549  0.016   6.622
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/12s]
 [11s/12s] OK
* 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
  ‘/home/biocbuild/bbs-3.0-bioc/meat/hiAnnotator.Rcheck/00check.log’
for details.

hiAnnotator.Rcheck/00install.out:

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

hiAnnotator.Rcheck/hiAnnotator-Ex.timings:

nameusersystemelapsed
cleanColname0.0000.0000.001
doAnnotation2.2640.0362.354
get2NearestFeature6.5490.0166.622
getFeatureCounts3.0800.0163.151
getFeatureCountsBig3.0800.0083.091
getLowestDists0.1160.0000.114
getNearestFeature2.6040.0042.676
getRelevantCol0.0080.0000.007
getSitesInFeature1.4760.0001.496
getUCSCtable000
getWindowLabel0.0040.0000.000
makeChunks0.7760.0000.788
makeGRanges0.8000.0080.901
makeUCSCsession0.0000.0000.001
plotdisFeature2.1610.0122.277