BioC 2.12: CHECK report for chimera on george2

Package: chimera

Version: 1.2.6

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings chimera_1.2.6.tar.gz

StartedAt: 2013-10-09 00:48:43 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:00:08 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 685.0 seconds

RetCode: 0

Status:  OK

CheckDir: chimera.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/chimera.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [36s/39s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [284s/306s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotCoverage     100.514  0.852 109.236
chimeraSeqs       42.022  0.552  46.198
class.fSet        38.347  0.472  41.965
fusionPeptides    38.163  0.496  40.759
filterList        12.560  0.024  14.053
fusionName        10.453  0.036  11.723
supportingReads    8.833  0.052   9.430
importFusionData   8.676  0.024   8.869
* 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
  ‘/home/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	42.022	0.552	46.198
class.fSet	38.347	0.472	41.965
filterList	12.560	0.024	14.053
fusionName	10.453	0.036	11.723
fusionPeptides	38.163	0.496	40.759
importFusionData	8.676	0.024	8.869
plotCoverage	100.514	0.852	109.236
subreadRun	0.556	2.460	3.182
supportingReads	8.833	0.052	9.430
tophatInstallation	0.004	0.000	0.005
tophatRun	0.000	0.004	0.006