BioC 3.0: CHECK report for exonfindR on perceval

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: 2014-10-12 00:24:26 -0700 (Sun, 12 Oct 2014)

EndedAt: 2014-10-12 00:33:31 -0700 (Sun, 12 Oct 2014)

EllapsedTime: 545.0 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-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 ... [35s/35s] 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 ... [165s/165s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
analyzeFeatures    48.967 13.979  65.825
predictTxFeatures  30.139  7.661  39.174
getSGFeatureCounts 18.544  7.655  25.951
* 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	0.196	0.012	0.209
SGFeatures	0.061	0.001	0.062
TxFeatures	0.075	0.001	0.076
TxVariantCounts	0.762	0.014	0.777
TxVariants	0.199	0.002	0.200
analyzeFeatures	48.967	13.979	65.825
analyzeVariants	2.789	0.057	2.878
annotate	2.920	0.010	2.948
assays	0.004	0.000	0.005
convertToSGFeatures	3.501	0.018	3.536
convertToTxFeatures	1.085	0.009	1.094
exportFeatures	0.001	0.001	0.001
filterTerminalExons	0.358	0.001	0.361
findTxVariants	2.439	0.004	2.451
getBamInfo	0.257	0.048	0.305
getSGFeatureCounts	18.544	7.655	25.951
getTxVariantCounts	0.110	0.031	0.140
mergeTxFeatures	0.785	0.010	0.797
plotFeatures	0.001	0.000	0.000
plotSpliceGraph	0.001	0.000	0.001
plotVariants	0.001	0.000	0.000
predictTxFeatures	30.139	7.661	39.174
slots	0.004	0.000	0.005