BioC 2.12: CHECK report for chimera on petty

Package: chimera

Version: 1.2.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chimera_1.2.6.tar.gz

StartedAt: 2013-10-08 21:54:17 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:06:53 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 756.7 seconds

RetCode: 0

Status:  OK

CheckDir: chimera.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/chimera.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'chimera/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chimera' version '1.2.6'
* 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 'chimera' can be installed ... [35s/35s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
subreadRun: no visible global function definition for 'buildindex'
subreadRun: no visible global function definition for 'align'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [417s/421s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotCoverage     177.945  2.113 182.077
fusionPeptides    57.063  0.839  58.286
chimeraSeqs       56.718  0.879  58.110
class.fSet        55.760  0.921  57.423
filterList        13.090  0.196  13.457
fusionName        11.087  0.125  11.349
supportingReads   10.051  0.134  10.229
importFusionData   9.741  0.158   9.976
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/chimera.Rcheck/00check.log'
for details.

* installing *source* package 'chimera' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chimera)

name	user	system	elapsed
chimeraSeqs	56.718	0.879	58.110
class.fSet	55.760	0.921	57.423
filterList	13.090	0.196	13.457
fusionName	11.087	0.125	11.349
fusionPeptides	57.063	0.839	58.286
importFusionData	9.741	0.158	9.976
plotCoverage	177.945	2.113	182.077
subreadRun	0.868	1.668	2.603
supportingReads	10.051	0.134	10.229
tophatInstallation	0.002	0.003	0.006
tophatRun	0.002	0.003	0.005