BioC 3.0: CHECK report for derfinder on perceval

Package: derfinder

Version: 1.0.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch derfinder_1.0.10.tar.gz

StartedAt: 2015-04-10 00:43:12 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:52:00 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 527.8 seconds

RetCode: 0

Status:  OK

CheckDir: derfinder.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 derfinder_1.0.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/derfinder.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [46s/51s] 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 ... [52s/52s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
coverageToExon   6.742  0.875   7.622
analyzeChr       6.106  0.181   6.374
makeGenomicState 5.579  0.064   5.817
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [0s/0s]
 [1s/1s] 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/derfinder.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
advancedArg	0.007	0.000	0.007
analyzeChr	6.106	0.181	6.374
annotateRegions	0.718	0.024	0.743
calculatePvalues	1.351	0.011	1.361
calculateStats	0.471	0.002	0.474
coerceGR	0.171	0.002	0.173
collapseFullCoverage	0.012	0.002	0.014
coverageToExon	6.742	0.875	7.622
createBw	0.378	0.004	0.383
createBwSample	0.141	0.002	0.144
extendedMapSeqlevels	0.123	0.011	0.134
filterData	0.468	0.020	0.489
findRegions	0.311	0.007	0.319
fullCoverage	0.406	0.020	0.425
getRegionCoverage	0.762	0.025	0.796
loadCoverage	0.217	0.016	0.233
makeGenomicState	5.579	0.064	5.817
makeModels	0.031	0.002	0.033
mergeResults	0.792	0.018	0.812
preprocessCoverage	0.466	0.003	0.469
rawFiles	0.009	0.002	0.010
regionMatrix	0.701	0.015	0.717
sampleDepth	0.031	0.001	0.031