Package: Genominator

Version: 1.8.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch Genominator_1.8.0.tar.gz

StartedAt: 2012-01-09 03:11:54 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 03:14:44 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 170.0 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/Genominator.Rcheck'
* using R version 2.14.1 (2011-12-22)
* 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 '1.8.0'
* 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 whether package 'Genominator' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 165.5Mb
  sub-directories of 1Mb or more:
    data    1.3Mb
    doc   161.2Mb
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.genominator.coverage':
  'plot.genominator.coverage'

S3 methods shown with full name in documentation object 'plot.genominator.goodness.of.fit':
  'plot.genominator.goodness.of.fit'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                        old_size new_size compress
  chr1_yeast.rda           528Kb    253Kb       xz
  yeastAnno.rda             79Kb     58Kb       xz
  yeastAnno.sources.rda    755Kb    218Kb       xz
* checking examples ... OK
* 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

* installing *source* package 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Genominator.Rnw' 
   'plotting.Rnw' 
   'withShortRead.Rnw' 
** testing if installed package can be loaded

* DONE (Genominator)

name	user	system	elapsed
ExpData	0	0	0
addPrimingWeights	6.25	0.67	7.13
aggregateExpData	2.28	0.00	2.28
applyMapped	1.47	0.00	1.47
collapseExpData	3.47	0.05	3.53
computeCoverage	1.22	0.03	1.26
computePrimingWeights	0.48	0.31	0.80
getRegion	0.33	0.00	0.33
importFromAlignedReads	0	0	0
importToExpData	0.75	0.00	0.75
joinExpData	5.76	0.03	5.82
makeGeneRepresentation	0.25	0.00	0.25
mergeWithAnnotation	0.69	0.00	0.69
plot.genominator.coverage	4.03	0.02	4.05
plot.genominator.goodness.of.fit	0.95	0.03	0.99
regionGoodnessOfFit-methods	0.91	0.00	0.90
splitByAnnotation	1.31	0.00	1.31
summarizeByAnnotation	0.70	0.03	0.74
summarizeExpData	0.78	0.00	0.78
validAnnotation	0.02	0.00	0.02
yeastAnno	0.15	0.03	0.18