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Package 61/436HostnameOS / ArchBUILDCHECKBUILD BIN
BSgenome 1.19.3
H. Pages
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BSgenome
Last Changed Rev: 52084 / Revision: 53255
Last Changed Date: 2011-01-26 13:56:14 -0800 (Wed, 26 Jan 2011)
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 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK [ OK ] OK 

Summary

Package: BSgenome
Version: 1.19.3
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BSgenome_1.19.3.tar.gz
StartedAt: 2011-02-24 15:13:10 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 15:16:18 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 188.2 seconds
RetCode: 0
Status:  OK 
CheckDir: BSgenome.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/BSgenome.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.19.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'BSgenome' 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 ... 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 ... NOTE
'library' or 'require' call not declared from: BSgenome.Scerevisiae.UCSC.sacCer1
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

BSgenome.Rcheck/00install.out:

* installing *source* package 'BSgenome' ...
** R
** inst
** preparing package for lazy loading

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

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (BSgenome)

BSgenome.Rcheck/BSgenome-Ex.timings:

nameusersystemelapsed
BSgenome-class1.7910.0471.886
BSgenome-utils45.513 0.80946.398
BSgenomeForge0.0190.0030.023
GenomeData-class0.0160.0010.016
GenomeDataList-class0.0470.0010.047
GenomeDescription-class0.0350.0020.037
available.genomes1.2270.2015.136
bsapply14.236 0.71115.030
gdreduce0.0010.0000.002
getSeq12.635 3.33715.987
injectSNPs13.032 0.56113.701