Package: Genominator

Version: 1.6.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch Genominator_1.6.0.tar.gz

StartedAt: 2011-10-20 14:35:46 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:38:19 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 152.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Genominator.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/Genominator.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Genominator' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 164.9Mb
  sub-directories of 1Mb or more:
    data    1.3Mb
    doc   160.6Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   Genominator.Rnw
   plotting.Rnw
   withShortRead.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/Genominator.Rcheck/00check.log'
for details

* installing *source* package 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Genominator)

name	user	system	elapsed
ExpData	0	0	0
addPrimingWeights	5.03	0.33	5.53
aggregateExpData	1.78	0.01	1.81
applyMapped	1.76	0.02	1.78
collapseExpData	2.99	0.03	3.02
computeCoverage	0.92	0.05	0.98
computePrimingWeights	0.47	0.34	0.81
getRegion	0.23	0.00	0.24
importFromAlignedReads	0	0	0
importToExpData	0.49	0.00	0.48
joinExpData	3.97	0.03	5.61
makeGeneRepresentation	0.28	0.00	0.28
mergeWithAnnotation	0.42	0.02	0.44
plot.genominator.coverage	2.83	0.01	2.89
plot.genominator.goodness.of.fit	0.79	0.04	1.33
regionGoodnessOfFit-methods	0.69	0.01	1.64
splitByAnnotation	0.89	0.03	0.92
summarizeByAnnotation	0.47	0.00	0.47
summarizeExpData	0.58	0.00	0.58
validAnnotation	0.01	0.00	0.01
yeastAnno	0.18	0.02	0.19