Package: Genominator

Version: 1.7.0

Command: mkdir Genominator.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Genominator.buildbin-libdir Genominator_1.7.0.tar.gz >Genominator-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=Genominator.buildbin-libdir --install="check:Genominator-install.out" --force-multiarch --no-vignettes --timings Genominator_1.7.0.tar.gz && mv Genominator.buildbin-libdir/* Genominator.Rcheck/ && rmdir Genominator.buildbin-libdir

StartedAt: 2011-07-07 05:07:08 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:12:32 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 323.9 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 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.7.0'
* checking package name space 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 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
* loading checks for arch 'i386'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or 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    221Kb       xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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

install for i386

* installing *source* package 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: DBI

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: biomaRt
Loading required package: grid
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Genominator.Rnw' 
   'plotting.Rnw' 
   'withShortRead.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'Genominator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Genominator' as Genominator_1.7.0.zip

* DONE (Genominator)

name	user	system	elapsed
ExpData	0	0	0
addPrimingWeights	4.43	0.32	5.03
aggregateExpData	1.29	0.02	1.31
applyMapped	1.69	0.00	1.80
collapseExpData	2.70	0.03	2.77
computeCoverage	0.87	0.03	0.91
computePrimingWeights	0.45	0.27	0.72
getRegion	0.2	0.0	0.2
importFromAlignedReads	0	0	0
importToExpData	0.43	0.00	0.42
joinExpData	3.99	0.01	4.32
makeGeneRepresentation	0.3	0.0	0.3
mergeWithAnnotation	0.42	0.00	0.42
plot.genominator.coverage	2.76	0.02	2.78
plot.genominator.goodness.of.fit	0.92	0.00	0.92
regionGoodnessOfFit-methods	0.81	0.05	0.85
splitByAnnotation	0.98	0.00	0.99
summarizeByAnnotation	0.44	0.00	0.79
summarizeExpData	0.53	0.01	0.54
validAnnotation	0.01	0.00	0.02
yeastAnno	0.19	0.02	0.20