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Package 177/419HostnameOS / ArchBUILDCHECKBUILD BIN
GGtools 3.8.4
Vince Carey
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/GGtools
Last Changed Rev: 51512 / Revision: 54281
Last Changed Date: 2010-12-13 12:32:55 -0800 (Mon, 13 Dec 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ ERROR ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GGtools
Version: 3.8.4
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings GGtools_3.8.4.tar.gz
StartedAt: 2011-03-31 06:19:37 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 06:27:22 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 465.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: GGtools.Rcheck
Warnings: NA

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/GGtools.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGtools/DESCRIPTION’ ... OK
* this is package ‘GGtools’ version ‘3.8.4’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘GGtools’ 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
bestCis: no visible binding for '<<-' assignment to ‘maxgap’
bestCis: no visible global function definition for ‘mclapply’
diagffCC: no visible global function definition for ‘mclapply’
diagffCC : <anonymous>: no visible binding for '<<-' assignment to ‘ex’
eqtlTests: no visible global function definition for ‘mclapply’
eqtlTestsMACH : <anonymous> : <anonymous>: no visible global function
  definition for ‘snp.rhs.testsMACH’
maxchisq: no visible global function definition for ‘mclapply’
sumScores2ff: no visible global function definition for ‘mclapply’
sumScores2ff : <anonymous>: no visible binding for '<<-' assignment to
  ‘ex’
min_p_vals,maxchisq-character-character-numeric : mtcorrp: no visible
  global function definition for ‘mt.rawp2adjp’
* 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 ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... ERROR
Running examples in ‘GGtools-Ex.R’ failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scoresInRanges
> ### Title: structured survey of eqtlTestsManager to retrieve scores cis to
> ###   genes
> ### Aliases: scoresInRanges
> ### Keywords: models
> 
> ### ** Examples
> 
> gl = GGtools:::geneLimits( anno="illuminaHumanv1.db" )
Loading required package: illuminaHumanv1.db
> egl = GGtools:::extendGR(gl, siz=5e5)
> data(hmceuB36.2021)
> gl20 = names(egl[ which(seqnames(egl) == "chr20") ] )[1:20]
> p2 = intersect( gl20, featureNames(hmceuB36.2021) )
> curd = getwd()
> setwd(tempdir())
> if (file.exists("foo"))system("rm -rf foo")
> ee = eqtlTests( hmceuB36.2021[ probeId(p2), ], ˜1, targdir="sir" )
> library(ceu1kg)
> data(ceu1kgMeta_20)
Warning in data(ceu1kgMeta_20) : data set 'ceu1kgMeta_20' not found
> ceu1kgMeta_20 = updateObject(ceu1kgMeta_20)
Execution halted

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
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: snpMatrix
Loading required package: survival
Loading required package: splines
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, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

Loading required package: RCurl
Loading required package: bitops
Loading required package: tools
Loading required package: bit
Loading package bit1.1-6

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


Attaching package: 'bit'

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

    xor

Loading package ff2.2-1

- getOption("fftempdir")=="/tmp/RtmprswwvE"

- 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")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system

Attaching package ff


Attaching package: 'ff'

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

    write.csv, write.csv2

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

    is.factor, is.ordered

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

* DONE (GGtools)

GGtools.Rcheck/GGtools-Ex.timings:

nameusersystemelapsed
X2chunk17.993 0.21218.339
bestCis19.486 0.12019.604
cisRanges0.3640.0080.385
cisSnpTests15.397 0.29616.211
degnerASE010.0080.0000.008
diagffCC13.584 0.08413.669
eqtlTests12.493 0.18412.715
eqtlTestsManager-class0.0000.0000.002
ex60.080.000.08