BioC 3.0: CHECK report for exonfindR on oaxaca

Package: exonfindR

Version: 0.99.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch exonfindR_0.99.1.tar.gz

StartedAt: 2014-10-11 22:37:36 -0700 (Sat, 11 Oct 2014)

EndedAt: 2014-10-11 22:43:48 -0700 (Sat, 11 Oct 2014)

EllapsedTime: 371.9 seconds

RetCode: 0

Status:  OK

CheckDir: exonfindR.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 exonfindR_0.99.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/exonfindR.Rcheck’
* using R version 3.1.1 Patched (2014-09-25 r66681)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘exonfindR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exonfindR’ version ‘0.99.1’
* 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 ‘exonfindR’ can be installed ... [26s/26s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘GenomicRanges:::extraColumnSlotsAsDF’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... NOTE
  'BiocParallel' did not register default BiocParallelParams:
    attempt to apply non-function
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [113s/113s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
analyzeFeatures    35.809  5.980  43.161
predictTxFeatures  22.353  3.543  28.604
getSGFeatureCounts 14.055  3.435  17.376
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/exonfindR.Rcheck/00check.log’
for details.

* installing *source* package ‘exonfindR’ ...
** 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 (exonfindR)

name	user	system	elapsed
SGFeatureCounts	0.162	0.006	0.168
SGFeatures	0.047	0.001	0.048
TxFeatures	0.069	0.000	0.069
TxVariantCounts	0.487	0.007	0.494
TxVariants	0.180	0.001	0.183
analyzeFeatures	35.809	5.980	43.161
analyzeVariants	2.318	0.023	2.342
annotate	2.622	0.007	2.632
assays	0.004	0.000	0.004
convertToSGFeatures	2.933	0.009	2.953
convertToTxFeatures	0.851	0.005	0.858
exportFeatures	0.001	0.000	0.000
filterTerminalExons	0.3	0.0	0.3
findTxVariants	2.245	0.004	2.253
getBamInfo	0.201	0.018	0.219
getSGFeatureCounts	14.055	3.435	17.376
getTxVariantCounts	0.099	0.015	0.114
mergeTxFeatures	0.579	0.003	0.583
plotFeatures	0.001	0.000	0.001
plotSpliceGraph	0.001	0.000	0.001
plotVariants	0.001	0.000	0.000
predictTxFeatures	22.353	3.543	28.604
slots	0.005	0.000	0.010