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Package 191/462HostnameOS / ArchBUILDCHECKBUILD BIN
Genominator 1.7.0
James Bullard
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Genominator
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: Genominator
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Genominator_1.7.0.tar.gz
StartedAt: 2011-05-09 14:50:50 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:53:42 -0700 (Mon, 09 May 2011)
EllapsedTime: 172.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Genominator.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/Genominator.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* 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  5.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.2Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘plotting.pdf’ from 719Kb to 129Kb
  consider running tools::compactPDF() on these files
* 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

Genominator.Rcheck/00install.out:

* 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

* DONE (Genominator)

Genominator.Rcheck/Genominator-Ex.timings:

nameusersystemelapsed
ExpData0.0020.0010.002
addPrimingWeights6.1820.1336.353
aggregateExpData1.5880.0261.633
applyMapped1.9090.1052.131
collapseExpData3.3580.1623.570
computeCoverage1.1610.0581.247
computePrimingWeights0.4800.0420.550
getRegion0.2180.0040.227
importFromAlignedReads000
importToExpData0.5000.0140.521
joinExpData4.0460.0724.317
makeGeneRepresentation0.4550.0060.547
mergeWithAnnotation0.4510.0060.469
plot.genominator.coverage3.6210.1453.967
plot.genominator.goodness.of.fit0.9720.0741.078
regionGoodnessOfFit-methods0.8880.0681.051
splitByAnnotation0.8700.0110.900
summarizeByAnnotation0.4660.0090.486
summarizeExpData0.6510.0140.668
validAnnotation0.0270.0020.030
yeastAnno0.3490.0180.374