Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 167/389HostnameOS / ArchBUILDCHECKBUILD BIN
girafe 1.0.0
J. Toedling
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/girafe
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / 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: girafe
Version: 1.0.0
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings girafe_1.0.0.tar.gz
StartedAt: 2010-10-04 17:53:11 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 17:56:23 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 192.5 seconds
RetCode: 0
Status:  OK 
CheckDir: girafe.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/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 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 ... 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

girafe.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'girafe' ...
** libs
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c coverage.cpp -o coverage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c girafe_init.c -o girafe_init.o
g++ -shared -L/usr/local/lib64 -o girafe.so coverage.o girafe_init.o -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/girafe.Rcheck/girafe/libs
** 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)

girafe.Rcheck/girafe-Ex.timings:

nameusersystemelapsed
AlignedGenomeIntervals-class8.6760.0768.771
fracOverlap0.2040.0480.271
intPhred0.0640.0000.066
negbinomsig21.078 0.01621.115
perWindow19.901 0.00419.907
plotAligned000
trimAdapter0.1120.0040.115
whichNearestMethods0.6080.0040.611