Hi all,

I am having the same problem as Lavinia (below), namely, the
arrayQualityMetrics() function failing on Windows. I'm using code directly
from the vignette:

> library("ALLMLL")
> data("MLL.A")
> library("arrayQualityMetrics")
> arrayQualityMetrics(expressionset = MLL.A,
+ outdir = "MLL",
+ force = TRUE,
+ do.logtransform = TRUE)

The result is:

The report will be written into directory 'MLL'.
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
(loaded the KernSmooth namespace)
[[1]]

[[2]]

[[3]]

Error in aqm.report.qm(p, obj[[i]], i, names(obj)[i]) :
  could not find function "svg"

> traceback()
4: aqm.report.qm(p, obj[[i]], i, names(obj)[i])
3: aqm.writereport(reporttitle, expressionset, obj)
2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE,
       do.logtransform = TRUE)
1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE,
       do.logtransform = TRUE)


> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hgu133acdf_2.7.0          ALLMLL_1.2.8
 arrayQualityMetrics_3.2.3
[4] vsn_3.18.0                affyPLM_1.26.0
 preprocessCore_1.12.0
[7] gcrma_2.22.0              affy_1.28.0               Biobase_2.10.0


loaded via a namespace (and not attached):
 [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0
beadarray_2.0.2
 [5] Biostrings_2.18.2    DBI_0.2-5            genefilter_1.32.0
 grid_2.12.0
 [9] hwriter_1.3          IRanges_1.8.6        KernSmooth_2.23-4
 lattice_0.19-13
[13] latticeExtra_0.6-14  limma_3.6.9          marray_1.28.0
 RColorBrewer_1.0-2
[17] RSQLite_0.9-4        simpleaffy_2.26.1    splines_2.12.0
stats4_2.12.0
[21] survival_2.35-8      SVGAnnotation_0.7-2  tools_2.12.0
XML_3.2-0.2
[25] xtable_1.5-6

Thanks,
Dan


On Thu, Nov 18, 2010 at 11:14 PM, Lavinia Gordon <lavinia.gordon@mcri.edu.au
> wrote:

>  Hi Dan,
> hmm, tried this, no luck:
> > arrayQualityMetrics(expressionset = methylumi.eset,outdir =
> "arrayQualityMetrics_patients", force = TRUE)
> The report will be written into directory 'arrayQualityMetrics_patients'.
> [[1]]
>
> [[2]]
>
>
> Error in aqm.report.qm(p, obj[[i]], i, names(obj)[i]) :
>   could not find function "svg"
> >
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
> LC_MONETARY=English_Australia.1252
> [4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] arrayQualityMetrics_3.2.3 vsn_3.18.0
> affyPLM_1.26.0            preprocessCore_1.12.0
>  [5] gcrma_2.22.0              affy_1.28.0
> SVGAnnotation_0.7-2       XML_3.2-0.1
>  [9] Cairo_1.4-5               methylumi_1.4.0
> lumi_2.2.0                Biobase_2.10.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0
> beadarray_2.0.1      Biostrings_2.18.0
>  [6] DBI_0.2-5            genefilter_1.32.0    grid_2.12.0
> hdrcde_2.15          hwriter_1.2
> [11] IRanges_1.8.2        KernSmooth_2.23-4    lattice_0.19-13
> latticeExtra_0.6-14  limma_3.6.4
> [16] marray_1.28.0        MASS_7.3-8           Matrix_0.999375-45
> mgcv_1.7-2           nlme_3.1-97
> [21] RColorBrewer_1.0-2   RSQLite_0.9-3        simpleaffy_2.26.0
> splines_2.12.0       stats4_2.12.0
> [26] survival_2.36-1      xtable_1.5-6
> >
>
>
> Any ideas?
> thanks
> Lavinia.
>
>
> On 19/11/2010 5:10 PM, Lavinia Gordon wrote:
>
> Thanks Dan, sorry I had missed the previous posts.
>
> On 19/11/2010 5:03 PM, Dan Tenenbaum wrote:
>
>
>
> On Thu, Nov 18, 2010 at 9:51 PM, Lavinia Gordon <
> lavinia.gordon@mcri.edu.au> wrote:
>
>> Hi,
>> I think there is a problem with the 2.7 version of arrayQualityMetrics.
>> Following the example (in the script
>> \R\R-2.12.0\library\arrayQualityMetrics\scripts\arrayQualityMetrics.R)
>>
>> > library("arrayQualityMetrics")
>> Loading required package: affyPLM
>> Loading required package: gcrma
>> Loading required package: preprocessCore
>>
>> Attaching package: 'affyPLM'
>>
>> The following object(s) are masked from 'package:stats':
>>
>>    resid, residuals, weights
>>
>> Loading required package: vsn
>> > arrayQualityMetrics(expressionset = MLL.A,
>> +                     outdir = "MLL",
>> +                     force = TRUE,
>> +                     do.logtransform = TRUE)
>> The directory 'MLL' has been created.
>> Error : cannot allocate vector of size 77.4 Mb
>> KernSmooth 2.23 loaded
>> Copyright M. P. Wand 1997-2009
>> (loaded the KernSmooth namespace)
>> [[1]]
>>
>> [[2]]
>>
>> [[3]]
>>
>> Error in aqm.report.qm(p, obj[[i]], i, names(obj)[i]) :
>>  could not find function "svg"
>> In addition: Warning message:
>> In arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force =
>> TRUE,  :
>>  Could not draw spatial distribution of intensities
>>
>> > traceback()
>> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i])
>> 3: aqm.writereport(reporttitle, expressionset, obj)
>> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force =
>> TRUE,
>>       do.logtransform = TRUE)
>> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force =
>> TRUE,
>>       do.logtransform = TRUE)
>>
>> > sessionInfo()
>> R version 2.12.0 (2010-10-15)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
>>  LC_MONETARY=English_Australia.1252
>> [4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] hgu133acdf_2.7.0          arrayQualityMetrics_3.2.0 vsn_3.18.0
>>        affyPLM_1.26.0
>> [5] preprocessCore_1.12.0     gcrma_2.22.0              ALLMLL_1.2.8
>>        affy_1.28.0
>> [9] Biobase_2.10.0
>>
>> loaded via a namespace (and not attached):
>>  [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0
>> beadarray_2.0.1      Biostrings_2.18.0
>>  [6] DBI_0.2-5            genefilter_1.32.0    grid_2.12.0
>>  hwriter_1.2          IRanges_1.8.2
>> [11] KernSmooth_2.23-4    lattice_0.19-13      latticeExtra_0.6-14
>>  limma_3.6.4          marray_1.28.0
>> [16] RColorBrewer_1.0-2   RSQLite_0.9-3        simpleaffy_2.26.0
>>  splines_2.12.0       stats4_2.12.0
>> [21] survival_2.36-1      SVGAnnotation_0.6-0  tools_2.12.0
>> XML_3.2-0.1          xtable_1.5-6
>>
>> with regards
>>
>> Lavinia Gordon
>>
>>  Hi Lavinia,
>
>  This is a known issue that has come up with this package before on this
> list. You need the current versions of arrayQualityMetrics (3.2.3) and
> SVGAnnotation (0.7-2).
> Try:
> biocLite(c("arrayQualityMetrics","SVGAnnotation"))
>
>  Dan
>
>
>
> --
> Senior Bioinformatics Officer
> Murdoch Childrens Research Institute
> Royal Children's Hospital
> Flemington Road
> Parkville
> Victoria 3052
> Australiawww.mcri.edu.au
>
>
>
> --
> Senior Bioinformatics Officer
> Murdoch Childrens Research Institute
> Royal Children's Hospital
> Flemington Road
> Parkville
> Victoria 3052
> Australiawww.mcri.edu.au
>
>

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