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Package 70/472HostnameOS / ArchBUILDCHECKBUILD BIN
BSgenome 1.21.3
H. Pages
Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BSgenome
Last Changed Rev: 56095 / Revision: 56351
Last Changed Date: 2011-06-09 23:49:52 -0700 (Thu, 09 Jun 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 
moscato1 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: BSgenome
Version: 1.21.3
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BSgenome_1.21.3.tar.gz
StartedAt: 2011-06-22 01:47:11 -0700 (Wed, 22 Jun 2011)
EndedAt: 2011-06-22 01:51:55 -0700 (Wed, 22 Jun 2011)
EllapsedTime: 284.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BSgenome.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/BSgenome.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.21.3’
* 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 installed package size ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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

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 ...
*** tangling vignette sources ...
   ‘BSgenomeForge.Rnw’ 
   ‘GenomeSearching.Rnw’ 
** testing if installed package can be loaded

* DONE (BSgenome)

BSgenome.Rcheck/BSgenome-Ex.timings:

nameusersystemelapsed
BSgenome-class2.2990.1042.465
BSgenome-utils59.881 1.87563.197
BSgenomeForge0.0250.0030.028
GenomeData-class0.0130.0010.014
GenomeDataList-class0.0650.0000.065
GenomeDescription-class0.0510.0030.055
available.genomes1.2420.3546.432
bsapply18.946 2.04724.988
gdreduce0.0030.0000.002
getSeq-methods16.888 8.30026.214
injectSNPs18.311 1.18220.351