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Package 178/419HostnameOS / ArchBUILDCHECKBUILD BIN
girafe 1.2.0
J. Toedling
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/girafe
Last Changed Rev: 50293 / Revision: 54588
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / 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 

Summary

Package: girafe
Version: 1.2.0
Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings girafe_1.2.0.tar.gz
StartedAt: 2011-04-07 07:16:25 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 07:20:27 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 242.5 seconds
RetCode: 0
Status:  OK  
CheckDir: girafe.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/girafe.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'girafe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'girafe' version '1.2.0'
* 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 'fraction1'
fracOverlap: no visible binding for global variable 'fraction2'
getFeatureCounts: no visible binding for global variable 'fraction1'
getFeatureCounts: no visible binding for global variable 'Index1'
intPhred: no visible binding for global variable 'mclapply'
oldAGIoverlap: no visible binding for global variable 'mclapply'
reduceOne: no visible binding for global variable 'fraction1'
reduceOne: no visible binding for global variable 'fraction2'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

girafe.Rcheck/00install.out:

* installing *source* package 'girafe' ...
** libs
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c coverage.cpp -o coverage.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/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˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-bioc/meat/girafe.Rcheck/girafe/libs/i386
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

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

    Map, cbind, eval, 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

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

* DONE (girafe)

girafe.Rcheck/girafe-Ex.timings:

nameusersystemelapsed
AlignedGenomeIntervals-class6.950.367.56
agiFromBam0.440.000.61
fracOverlap0.220.000.22
intPhred0.400.280.72
negbinomsig19.77 0.5720.39
perWindow18.81 0.1119.01
plotAligned0.160.000.16
trimAdapter0.510.290.88
whichNearestMethods1.250.151.53