BioC 3.5: CHECK report for derfinder on oaxaca

Package: derfinder

Version: 1.9.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings derfinder_1.9.8.tar.gz

StartedAt: 2017-03-04 01:43:18 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:52:40 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 562.1 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_1.9.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/derfinder.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.9.8’
* 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 ... 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.
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       8.478  1.284  10.033
makeGenomicState 5.050  0.037   5.127
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘RefManageR’
* 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-3.5-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	2.399	0.067	2.484
annotateRegions	0.922	0.010	0.933
calculatePvalues	1.383	0.009	1.393
calculateStats	0.257	0.002	0.259
coerceGR	0.118	0.002	0.118
collapseFullCoverage	0.009	0.001	0.010
coverageToExon	2.992	0.387	3.379
createBw	0.254	0.002	0.256
createBwSample	0.075	0.001	0.077
define_cluster	0.009	0.000	0.010
derfinder-deprecated	0.003	0.000	0.004
extendedMapSeqlevels	0.160	0.009	0.170
filterData	0.254	0.006	0.261
findRegions	0.337	0.005	0.341
fullCoverage	0.751	0.012	0.763
getRegionCoverage	0.390	0.011	0.445
getTotalMapped	0.251	0.003	0.255
loadCoverage	0.194	0.012	0.207
makeGenomicState	5.050	0.037	5.127
makeModels	0.037	0.001	0.038
mergeResults	0.516	0.012	0.528
preprocessCoverage	0.115	0.001	0.117
railMatrix	8.478	1.284	10.033
rawFiles	0.003	0.000	0.004
regionMatrix	0.416	0.007	0.424
sampleDepth	0.021	0.000	0.022