ceu1kg 0.0.16
VJ Carey
| Snapshot Date: 2010-11-12 00:25:07 -0800 (Fri, 12 Nov 2010) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ceu1kg | | Last Changed Rev: 1384 / Revision: 1384 | | Last Changed Date: 2010-11-10 20:10:20 -0800 (Wed, 10 Nov 2010) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ ERROR ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | TIMEOUT | OK |
* using log directory 'E:/biocbld/bbs-2.8-data-experiment/meat/ceu1kg.Rcheck'
* using R version 2.13.0 Under development (unstable) (2010-11-10 r53547)
* 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 '0.0.16'
* 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 ...Warning: running command '"E:\biocbld\bbs-2.8-bioc\R/bin/i386/Rterm.exe" --vanilla --slave -f E:\biocbld\bbs-2.8-data-experiment\tmpdir\RtmpHJWeHe\Rin51f2734a' had status 1
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 8.1 Mb
Execution halted