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BioC 3.0: CHECK report for derfinder on zin1

This page was generated on 2015-04-10 09:42:39 -0700 (Fri, 10 Apr 2015).

Package 234/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
derfinder 1.0.10
Leonardo Collado-Torres
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/derfinder
Last Changed Rev: 97075 / Revision: 102249
Last Changed Date: 2014-11-24 13:36:38 -0800 (Mon, 24 Nov 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: derfinder
Version: 1.0.10
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings derfinder_1.0.10.tar.gz
StartedAt: 2015-04-09 23:13:55 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:19:02 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 307.5 seconds
RetCode: 0
Status:  OK 
CheckDir: derfinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings derfinder_1.0.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/derfinder.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 ‘derfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘derfinder’ version ‘1.0.10’
* 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 ‘derfinder’ can be installed ... [28s/29s] 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 objects imported by ':::' calls:
  ‘GenomeInfoDb:::.guessSpeciesStyle’
  ‘GenomeInfoDb:::.supportedSeqnameMappings’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/31s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [0s/0s]
 [0s/0s] 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/derfinder.Rcheck/00check.log’
for details.

derfinder.Rcheck/00install.out:

* installing *source* package ‘derfinder’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (derfinder)

derfinder.Rcheck/derfinder-Ex.timings:

nameusersystemelapsed
advancedArg0.0040.0000.004
analyzeChr4.2690.0724.357
annotateRegions0.4800.0080.489
calculatePvalues0.9200.0080.943
calculateStats0.3200.0000.319
coerceGR0.1040.0000.104
collapseFullCoverage0.0120.0000.011
coverageToExon3.7560.2844.043
createBw0.2080.0000.210
createBwSample0.0880.0000.089
extendedMapSeqlevels0.10.00.1
filterData0.2360.0000.234
findRegions0.1800.0000.182
fullCoverage0.2840.0040.287
getRegionCoverage0.4000.0160.414
loadCoverage0.1720.0040.176
makeGenomicState3.6640.0403.783
makeModels0.0280.0000.036
mergeResults0.6320.0040.659
preprocessCoverage0.3760.0040.383
rawFiles0.0040.0040.006
regionMatrix0.4200.0080.427
sampleDepth0.0240.0000.026