BioC 2.13: CHECK report for chimera on zin1

Package: chimera

Version: 1.4.6

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings chimera_1.4.6.tar.gz

StartedAt: 2014-04-05 00:10:36 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:18:55 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 498.9 seconds

RetCode: 0

Status:  OK

CheckDir: chimera.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/chimera.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.4.6’
* 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 ... [18s/18s] 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:
  ‘BSgenome.Hsapiens.UCSC.hg19’ ‘Biobase’ ‘Rsamtools’
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ‘methods’ ‘org.Hs.eg.db’
  ‘org.Mm.eg.db’
  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 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 ... [325s/326s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
fusionPeptides   85.626  1.448  87.591
plotCoverage     76.312  0.036  76.543
chimeraSeqSet    50.375  0.816  51.281
class.fSet       26.609  0.116  26.912
chimeraSeqs      25.470  0.120  25.631
prettyPrint       9.453  0.000   9.495
filterList        8.357  0.016   8.385
fusionName        7.784  0.008   7.828
supportingReads   7.745  0.012   7.791
is.fSet           6.977  0.008   6.999
importFusionData  6.936  0.032   6.993
* 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
  ‘/home/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	0.012	0.000	0.014
bam2fastq	0.008	0.000	0.009
chimeraSeqSet	50.375	0.816	51.281
chimeraSeqs	25.470	0.120	25.631
class.fSet	26.609	0.116	26.912
filterList	8.357	0.016	8.385
filterSamReads	0.004	0.000	0.001
fusionName	7.784	0.008	7.828
fusionPeptides	85.626	1.448	87.591
gapfillerInstallation	0.000	0.000	0.001
gapfillerRun	0	0	0
gapfillerWrap	0.000	0.000	0.001
importFusionData	6.936	0.032	6.993
is.fSet	6.977	0.008	6.999
picardInstallation	0.004	0.000	0.001
plotCoverage	76.312	0.036	76.543
prettyPrint	9.453	0.000	9.495
removingErrorLine	0.000	0.000	0.001
starInstallation	0.000	0.000	0.001
starReads	0.000	0.000	0.001
starRun	0	0	0
subreadRun	0.536	0.860	1.410
supportingReads	7.745	0.012	7.791
tophatInstallation	0.000	0.000	0.001
tophatRun	0.000	0.004	0.002
validateSamFile	0.000	0.000	0.002