Package: ceu1kg

Version: 0.0.15

Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings ceu1kg_0.0.15.tar.gz

StartedAt: 2010-11-09 14:15:13 -0800 (Tue, 09 Nov 2010)

EndedAt: 2010-11-09 14:23:40 -0800 (Tue, 09 Nov 2010)

EllapsedTime: 506.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: ceu1kg.Rcheck

Warnings: NA

* using log directory 'E:/biocbld/bbs-2.7-data-experiment/meat/ceu1kg.Rcheck'
* using R version 2.12.0 RC (2010-10-11 r53293)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ceu1kg/DESCRIPTION' ... OK
* this is package 'ceu1kg' version '0.0.15'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ceu1kg' can be installed ... OK
* 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 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 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 ... NOTE
  Error: cannot allocate vector of size 2.3 Mb
  Call sequence:
  2: load(zfile, envir = envir)
  1: utils::data(list = f, package = character(0L), envir = dataEnv)
  Execution halted
* checking examples ... ERROR
Running examples in 'ceu1kg-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ceu1kg-package
> ### Title: CEU (N=60) genotypes from 1000 genomes pilot phase I
> ### Aliases: ceu1kg-package ceu1kg
> ### Keywords: package
> 
> ### ** Examples
> 
> # all genotypes
> library(ceu1kg)
> data(ceu1kg.sml)
> names(ceu1kg.sml)
 [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9" 
[10] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18"
[19] "chr19" "chr20" "chr21" "chr22"
> ceu1kg.sml[[1]]
A snp.matrix with  60 rows and  605756 columns
Row names:  NA06985 ... NA12874 
Col names:  chr1:533 ... chr1:247196267 
> data(ceu1kgMeta_20)
> ceu1kgMeta_20
GRanges with 174484 ranges and 3 elementMetadata values
               seqnames               ranges strand   |         ref         alt
                  <Rle>            <IRanges>  <Rle>   | <character> <character>
     rs6078030    chr20       [ 9098,  9098]      *   |           C           T
     rs4814683    chr20       [ 9795,  9795]      *   |           G           T
    rs34147676    chr20       [10731, 10731]      *   |           C           A
     rs6139074    chr20       [11244, 11244]      *   |           A           C
   chr20:11541    chr20       [11541, 11541]      *   |           C           A
     rs1418258    chr20       [11799, 11799]      *   |           C           T
    rs13043000    chr20       [13288, 13288]      *   |           G           T
   chr20:13532    chr20       [13532, 13532]      *   |           G           T
     rs6053810    chr20       [13900, 13900]      *   |           G           A
           ...      ...                  ...    ... ...         ...         ...
chr20:62421836    chr20 [62421836, 62421836]      *   |           G           A
chr20:62424001    chr20 [62424001, 62424001]      *   |           G           A
    rs62218003    chr20 [62424076, 62424076]      *   |           C           A
chr20:62424344    chr20 [62424344, 62424344]      *   |           C           T
    rs62218006    chr20 [62430673, 62430673]      *   |           T           C
    rs11698187    chr20 [62430736, 62430736]      *   |           A           G
chr20:62431623    chr20 [62431623, 62431623]      *   |           A           G
     rs4057205    chr20 [62433647, 62433647]      *   |           C           T
     rs7270744    chr20 [62434810, 62434810]      *   |           T           G
                   depth
               <numeric>
     rs6078030       192
     rs4814683        NA
    rs34147676       228
     rs6139074        NA
   chr20:11541       331
     rs1418258        NA
    rs13043000        NA
   chr20:13532       219
     rs6053810       325
           ...       ...
chr20:62421836       202
chr20:62424001       379
    rs62218003       354
chr20:62424344       169
    rs62218006       368
    rs11698187       345
chr20:62431623       326
     rs4057205       380
     rs7270744       388

seqlengths
 chr20
    NA
> data(ceu1kg)
Warning in load(zfile, envir = envir) :
  Reached total allocation of 1535Mb: see help(memory.size)
Warning in load(zfile, envir = envir) :
  Reached total allocation of 1535Mb: see help(memory.size)
Warning in load(zfile, envir = envir) :
  Reached total allocation of 1535Mb: see help(memory.size)
Warning in load(zfile, envir = envir) :
  Reached total allocation of 1535Mb: see help(memory.size)
Error: cannot allocate vector of size 9.8 Mb
Execution halted

* installing *source* package 'ceu1kg' ...
** data
** inst
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ceu1kg)

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