BioC 3.3: CHECK report for derfinder on morelia

Package: derfinder

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings derfinder_1.5.0.tar.gz

StartedAt: 2015-10-22 05:19:24 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 05:22:42 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 198.1 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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.5.0’
* 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 ‘derfinder’ can be installed ... [16s/17s] 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
'library' or 'require' call to ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... [20s/20s] 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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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	0.006	0.001	0.005
analyzeChr	0.824	0.011	0.835
annotateRegions	0.389	0.007	0.395
calculatePvalues	0.634	0.004	0.638
calculateStats	0.232	0.000	0.233
coerceGR	0.096	0.002	0.097
collapseFullCoverage	0.014	0.002	0.014
coverageToExon	2.352	0.340	2.694
createBw	0.224	0.004	0.228
createBwSample	0.130	0.015	0.146
extendedMapSeqlevels	0.116	0.018	0.135
filterData	0.177	0.013	0.189
findRegions	0.119	0.002	0.121
fullCoverage	0.309	0.009	0.319
getRegionCoverage	0.375	0.009	0.404
loadCoverage	0.135	0.007	0.142
makeGenomicState	2.870	0.028	2.917
makeModels	0.021	0.000	0.021
mergeResults	0.318	0.010	0.327
preprocessCoverage	0.081	0.001	0.081
rawFiles	0.003	0.001	0.004
regionMatrix	0.778	0.084	0.863
sampleDepth	0.019	0.000	0.019