BioC 3.4: CHECK report for derfinder on zin1

Package: derfinder

Version: 1.7.12

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings derfinder_1.7.12.tar.gz

StartedAt: 2016-09-20 05:28:35 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:35:15 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 400.4 seconds

RetCode: 0

Status:  OK

CheckDir: derfinder.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings derfinder_1.7.12.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/derfinder.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-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 ‘1.7.12’
* 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 7.644  0.124   7.867
* 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
  ‘/home/biocbuild/bbs-3.4-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	0.004	0.000	0.003
analyzeChr	0.940	0.012	0.955
annotateRegions	0.324	0.004	0.329
calculatePvalues	0.404	0.008	0.410
calculateStats	0.132	0.004	0.137
coerceGR	0.064	0.000	0.066
collapseFullCoverage	0.008	0.000	0.008
coverageToExon	2.216	0.896	3.112
createBw	0.116	0.000	0.116
createBwSample	0.048	0.000	0.048
extendedMapSeqlevels	0.088	0.004	0.093
filterData	0.140	0.000	0.142
findRegions	0.252	0.004	0.254
fullCoverage	0.224	0.000	0.225
getRegionCoverage	0.224	0.004	0.241
loadCoverage	0.128	0.004	0.132
makeGenomicState	2.732	0.008	2.746
makeModels	0.024	0.000	0.024
mergeResults	0.288	0.016	0.302
preprocessCoverage	0.132	0.000	0.131
railMatrix	7.644	0.124	7.867
rawFiles	0.004	0.000	0.003
regionMatrix	0.300	0.008	0.308
sampleDepth	0.020	0.000	0.022