BioC 3.1: CHECK report for exonfindR on petty

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 22:14:51 -0700 (Sat, 11 Oct 2014)

EndedAt: 2014-10-11 22:26:10 -0700 (Sat, 11 Oct 2014)

EllapsedTime: 679.8 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-3.1-bioc/meat/exonfindR.Rcheck’
* using R Under development (unstable) (2014-10-07 r66723)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [43s/47s] 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 ... OK
* 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 ... [173s/185s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
analyzeFeatures    54.140 13.287  76.666
predictTxFeatures  28.428  6.994  38.909
getSGFeatureCounts 19.709  7.132  26.732
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.1-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	0.267	0.014	0.334
SGFeatures	0.082	0.000	0.100
TxFeatures	0.104	0.000	0.121
TxVariantCounts	0.827	0.002	0.942
TxVariants	0.266	0.008	0.324
analyzeFeatures	54.140	13.287	76.666
analyzeVariants	3.221	0.082	3.381
annotate	3.345	0.008	3.428
assays	0.005	0.000	0.005
convertToSGFeatures	3.784	0.016	3.859
convertToTxFeatures	1.145	0.010	1.174
exportFeatures	0.001	0.000	0.001
filterTerminalExons	0.375	0.001	0.377
findTxVariants	2.799	0.006	2.833
getBamInfo	0.282	0.032	0.315
getSGFeatureCounts	19.709	7.132	26.732
getTxVariantCounts	0.096	0.019	0.116
mergeTxFeatures	0.795	0.046	0.873
plotFeatures	0.001	0.000	0.001
plotSpliceGraph	0.001	0.001	0.001
plotVariants	0.001	0.000	0.001
predictTxFeatures	28.428	6.994	38.909
slots	0.007	0.001	0.007