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Package 28/98HostnameOS / ArchBUILDCHECKBUILD BIN
encoDnaseI 0.1.7
VJ Carey
Snapshot Date: 2011-07-06 11:15:18 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/encoDnaseI
Last Changed Rev: 1520 / Revision: 1678
Last Changed Date: 2011-04-07 21:24:31 -0700 (Thu, 07 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: encoDnaseI
Version: 0.1.7
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch encoDnaseI_0.1.7.tar.gz
StartedAt: 2011-07-06 15:17:15 -0700 (Wed, 06 Jul 2011)
EndedAt: 2011-07-06 15:23:19 -0700 (Wed, 06 Jul 2011)
EllapsedTime: 363.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: encoDnaseI.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.9-data-experiment/meat/encoDnaseI.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'encoDnaseI/DESCRIPTION' ... OK
* this is package 'encoDnaseI' version '0.1.7'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'encoDnaseI' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.5Mb
* 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
ALICOR: no visible binding for global variable 'rawCD4'
WRC: no visible binding for global variable 'd19'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  'sOSR2'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'SNPlocs.Hsapiens.dbSNP.20090506'
* 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

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.9-data-experiment/meat/encoDnaseI.Rcheck/00check.log'
for details

encoDnaseI.Rcheck/00install.out:

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

Welcome to Bioconductor

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

Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: splines
Loading required package: Matrix

Attaching package: 'Matrix'

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

    det

Loading required package: RSQLite
Loading required package: DBI
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges

Attaching package: 'IRanges'

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

    updateObject

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

Loading required package: rtracklayer
Loading required package: RCurl
Loading required package: bitops
Loading required package: org.Hs.eg.db

Loading required package: GenomicRanges
Loading package bit1.1-7

package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)

creators: bit bitwhich

coercion: as.logical as.integer as.bit as.bitwhich which

operator: ! & | xor != == 

querying: print length any all min max range sum summary

bit access: length<- [ [<- [[ [[<-

for more help type ?bit

Loading package ff2.2-2
- getOption("fftempdir")=="E:/biocbld/bbs-2.9-data-experiment/tmpdir/RtmpGe3Ggg"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16095641.6 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==804782080 -- consider a different value for tuning your system


Attaching package: 'GGtools'

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

    geneNames

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'dnaseUse.Rnw' 
** testing if installed package can be loaded

* DONE (encoDnaseI)

encoDnaseI.Rcheck/encoDnaseI-Ex.timings:

nameusersystemelapsed
encoDnaseI4.720.025.06
hg18track-class7.560.047.78
juxtaPlot000