BioC 2.13: CHECK report for chimera on perceval

Package: chimera

Version: 1.4.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chimera_1.4.6.tar.gz

StartedAt: 2014-04-05 00:11:51 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:25:08 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 796.5 seconds

RetCode: 0

Status:  OK

CheckDir: chimera.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/chimera.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.6’
* 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 ... [31s/31s] 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘org.Mm.eg.db’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘BSgenome.Hsapiens.UCSC.hg19’ ‘methods’ ‘org.Hs.eg.db’
  ‘org.Mm.eg.db’ ‘Rsamtools’ ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... NOTE
.detectIntronic: no visible global function definition for ‘.onlyExons’
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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘chimera.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [495s/495s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
fusionPeptides   120.382 10.692 131.335
plotCoverage     106.861  0.681 107.614
chimeraSeqSet     76.183  3.628  79.890
class.fSet        38.180  0.784  38.988
chimeraSeqs       37.419  0.831  38.282
filterList        15.177  0.218  15.418
prettyPrint       14.952  0.146  15.108
is.fSet           12.484  0.121  12.689
fusionName        12.124  0.169  12.367
supportingReads   11.343  0.212  11.560
importFusionData  11.086  0.247  11.520
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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
MHmakeRandomString	0.015	0.005	0.020
bam2fastq	0.023	0.004	0.027
chimeraSeqSet	76.183	3.628	79.890
chimeraSeqs	37.419	0.831	38.282
class.fSet	38.180	0.784	38.988
filterList	15.177	0.218	15.418
filterSamReads	0.002	0.004	0.006
fusionName	12.124	0.169	12.367
fusionPeptides	120.382	10.692	131.335
gapfillerInstallation	0.002	0.003	0.005
gapfillerRun	0.002	0.004	0.007
gapfillerWrap	0.003	0.005	0.008
importFusionData	11.086	0.247	11.520
is.fSet	12.484	0.121	12.689
picardInstallation	0.002	0.003	0.006
plotCoverage	106.861	0.681	107.614
prettyPrint	14.952	0.146	15.108
removingErrorLine	0.002	0.003	0.005
starInstallation	0.002	0.004	0.006
starReads	0.002	0.003	0.005
starRun	0.002	0.003	0.005
subreadRun	1.471	2.487	4.007
supportingReads	11.343	0.212	11.560
tophatInstallation	0.002	0.003	0.005
tophatRun	0.002	0.004	0.006
validateSamFile	0.002	0.003	0.006