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Package 203/479HostnameOS / ArchBUILDCHECKBUILD BIN
GGtools 3.11.31
Vince Carey
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools
Last Changed Rev: 56132 / Revision: 56603
Last Changed Date: 2011-06-13 03:37:12 -0700 (Mon, 13 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  ERROR  ERROR 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: GGtools
Version: 3.11.31
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GGtools_3.11.31.tar.gz
StartedAt: 2011-07-07 02:04:02 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 02:15:01 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 658.9 seconds
RetCode: 0
Status:  OK  
CheckDir: GGtools.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/GGtools.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 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '3.11.31'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: multicore
* checking if this is a source package ... OK
* checking whether package 'GGtools' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 67.3Mb
  sub-directories of 1Mb or more:
    browserTrack   1.8Mb
    data          49.6Mb
    doc           10.5Mb
    GGEXsite       1.0Mb
    pup            2.0Mb
* 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
ieqtlTests: no visible global function definition for 'mclapply'
topKfeats: no visible binding for global variable 'i1'
topKfeats: no visible binding for global variable 'i2'
* checking Rd files ... NOTE
prepare_Rd: transScores.Rd:84-86: Dropping empty section \details
* 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 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 tests ... OK
* checking tests ...
  Running 'eqtest.R'
 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

GGtools.Rcheck/00install.out:

* installing *source* package 'GGtools' ...
** 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: snpStats
Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

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

    det

Loading required package: RSQLite
Loading required package: DBI
Loading required package: AnnotationDbi

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: RCurl
Loading required package: bitops

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-bioc/tmpdir/RtmpSGKlpN"

- 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

in method for 'coerce' with signature '"multffManager","eqtlTestsManager"': no definition for class "multffManager"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GGtools_2011.Rnw' 
   'binf09supp.Rnw' 
   'external.Rnw' 
** testing if installed package can be loaded

* DONE (GGtools)

GGtools.Rcheck/GGtools-Ex.timings:

nameusersystemelapsed
X2chunk000
cisProxScores-class000
cisProxScores45.45 0.3846.81
clipPCs71.44 0.7372.98
degnerASE010.000.020.02
dropMonomorphies2.840.042.89
eqtlTests15.64 0.1120.17
eqtlTestsManager-class000
ex60.060.000.06