Package: girafe

Version: 1.0.0

Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings girafe_1.0.0.tar.gz

StartedAt: 2010-10-04 18:27:30 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:30:53 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 203.6 seconds

RetCode: 0

Status:  OK

CheckDir: girafe.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/girafe.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'girafe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'girafe' version '1.0.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'girafe' can be installed ... OK
* 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 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 ... NOTE
fracOverlap: no visible binding for global variable 'fraction'
intPhred: no visible binding for global variable 'mclapply'
oldAGIoverlap: no visible binding for global variable 'mclapply'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'girafe' ...
** libs
  making DLL ...
g++ -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c coverage.cpp -o coverage.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O3 -Wall  -std=gnu99 -c girafe_init.c -o girafe_init.o
g++ -shared -s -static-libgcc -o girafe.dll tmp.def coverage.o girafe_init.o -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/girafe.Rcheck/girafe/libs
  ... done
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

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

    Map, cbind, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
    rbind, rep.int, table

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools

Attaching package: 'intervals'

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

    type

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

    reduce

Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.


Attaching package: 'Biobase'

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

    updateObject


Attaching package: 'genomeIntervals'

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

    strand, strand<-

Creating a new generic function for "plot" in "girafe"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (girafe)

name	user	system	elapsed
AlignedGenomeIntervals-class	7.57	0.37	9.50
fracOverlap	0.24	0.00	0.25
intPhred	0.45	0.25	0.70
negbinomsig	21.17	0.26	21.63
perWindow	20.83	0.17	21.03
plotAligned	0	0	0
trimAdapter	0.57	0.24	0.83
whichNearestMethods	1.04	0.16	1.21