BioC 3.6: CHECK report for derfinder on veracruz1

Package: derfinder

Version: 1.11.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings derfinder_1.11.6.tar.gz

StartedAt: 2017-08-16 02:08:09 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:17:07 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 537.4 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 derfinder_1.11.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/derfinder.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.11.6’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
* 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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.smootherFstats’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
railMatrix 7.723   1.01   9.019
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-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
analyzeChr	2.281	0.060	2.424
annotateRegions	0.731	0.010	0.767
calculatePvalues	1.183	0.009	1.224
calculateStats	0.179	0.001	0.183
coerceGR	0.104	0.001	0.111
collapseFullCoverage	0.011	0.002	0.012
coverageToExon	2.763	0.305	3.165
createBw	0.217	0.002	0.226
createBwSample	0.056	0.001	0.057
define_cluster	0.006	0.000	0.006
derfinder-deprecated	0.003	0.001	0.003
extendedMapSeqlevels	0.110	0.005	0.124
filterData	0.278	0.025	0.318
findRegions	0.314	0.035	0.368
fullCoverage	0.686	0.010	0.714
getRegionCoverage	0.312	0.009	0.338
getTotalMapped	0.172	0.000	0.177
loadCoverage	0.150	0.003	0.153
makeGenomicState	4.377	0.025	4.546
makeModels	0.024	0.000	0.024
mergeResults	0.419	0.010	0.444
preprocessCoverage	0.150	0.002	0.152
railMatrix	7.723	1.010	9.019
rawFiles	0.004	0.001	0.004
regionMatrix	0.394	0.008	0.406
sampleDepth	0.019	0.000	0.020