[Bioc-devel] [BioC] arrayQualityMetrics bug
Wolfgang Huber
whuber at embl.de
Tue Dec 14 15:25:28 CET 2010
Hi Dan, Lavinia
there are three solutions, in order of preference:
1. upgrade your R so that it contains the 'svg' graphics device (you can
test this with 'capabilities()'). AfaIu, this requires that you install
the libcairo system library (more specific instructions from a Windows
user are welcome - I currently lack the resources to check this.).
2. use an older version of arrayQualityMetrics,
http://www.bioconductor.org/packages/2.6/bioc/html/arrayQualityMetrics.html
which works fine with R 2.12 and does not use the svg device.
3. wait until I have fixed the devel version of arrayQualityMetrics (I
hope this will be over the Christmas break) and then use that. This will
run on Rs with and without svg, although with inferior functionality in
the latter case.
Best wishes
Wolfgang
Dan Tenenbaum scripsit 13/12/10 20:34:
> 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 at 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 at 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
>>
>>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
More information about the Bioc-devel
mailing list