[BioC] svg error in arrayQualityMetrics

[Andrzej Oleś]

Dear Juerg,

the error message is most probably due to an incompatibility with the
recent Cairo libraries, which has been fixed in the devel version
3.19.2 of 'arrayQualityMetrics'.

As already suggested by Wolfgang, please check whether switching to
the newest version resolves the issue.

Cheers,
Andrzej

On Fri, Mar 7, 2014 at 7:17 PM, Straubhaar, Juerg
<Juerg.Straubhaar at umassmed.edu> wrote:
> I am running the arrayQualityMetrics with:
>
> arrayQualityMetrics(expressionset=esett,outdir="TestAQM",force=TRUE,do.logtransform=FALSE,intgroup="SomeCategory")
>
> and get the following errror:
>
> Error in tmp[i] : invalid subscript type 'list'
>
> The error is generated in a 'brittle' part of the arrayQualityMetrics code on line 31 of the annotateSvgMapPlot.R source file, in the function annotateSvgPlot().
> Line 31 of this file is prepended with a comment pointing to the 'brittle' nature of this part of the code and says
>
> '...getPlotObjNodes' will be 'getMatplotSeries' or 'getPlotPoints' from
>     ## 'SVGAnnotation', which rely on conventions used by libcairo ...
>
> I replaced getPlotObjNodes in annotateSvgPlot() with getMatplotSeries() and getPlotPoints() to no avail.
>
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] grDevices datasets  parallel  stats     graphics  utils     methods
> [8] base
>
> other attached packages:
> [1] arrayQualityMetrics_3.18.0 AnnotationDbi_1.24.0
> [3] Biobase_2.22.0             BiocGenerics_0.8.0
> [5] RSQLite_0.11.4             DBI_0.2-7
>
> loaded via a namespace (and not attached):
>  [1] AnnotationForge_1.4.4    BSgenome_1.30.0          BeadDataPackR_1.14.0
>  [4] BiocInstaller_1.12.0     Biostrings_2.30.1        Cairo_1.5-5
>  [7] Category_2.28.0          DESeq2_1.2.10            DO.db_2.7
> [10] DOSE_2.0.0               Formula_1.1-1            GO.db_2.10.1
> [13] GOSemSim_1.20.3          GOstats_2.28.0           GSEABase_1.24.0
> [16] GenomicFeatures_1.14.3   GenomicRanges_1.14.4     Hmisc_3.14-3
> [19] IRanges_1.20.7           KEGG.db_2.10.1           KernSmooth_2.23-10
> [22] MASS_7.3-29              Matrix_1.1-2-2           PFAM.db_2.10.1
> [25] R.methodsS3_1.6.1        R.oo_1.18.0              R.utils_1.29.8
> [28] RBGL_1.38.0              RColorBrewer_1.0-5       RCurl_1.95-4.1
> [31] Rcpp_0.11.0              RcppArmadillo_0.4.100.0  ReportingTools_2.2.0
> [34] Rsamtools_1.14.3         SVGAnnotation_0.93-1     VariantAnnotation_1.8.12
> [37] XML_3.98-1.1             XVector_0.2.0            affy_1.40.0
> [40] affyPLM_1.38.0           affyio_1.30.0            annotate_1.40.1
> [43] beadarray_2.12.0         biomaRt_2.18.0           biovizBase_1.10.8
> [46] bitops_1.0-6             cluster_1.14.4           clusterProfiler_1.10.1
> [49] colorspace_1.2-4         dichromat_2.0-0          digest_0.6.4
> [52] edgeR_3.4.2              gcrma_2.34.0             genefilter_1.44.0
> [55] ggbio_1.10.12            ggplot2_0.9.3.1          graph_1.40.1
> [58] grid_3.0.2               gridExtra_0.9.1          gtable_0.1.2
> [61] hwriter_1.3              igraph_0.7.0             labeling_0.2
> [64] lattice_0.20-27          latticeExtra_0.6-26      limma_3.18.13
> [67] locfit_1.5-9.1           munsell_0.4.2            plyr_1.8.1
> [70] preprocessCore_1.24.0    proto_0.3-10             qvalue_1.36.0
> [73] reshape2_1.2.2           rtracklayer_1.22.4       scales_0.2.3
> [76] setRNG_2011.11-2         splines_3.0.2            stats4_3.0.2
> [79] stringr_0.6.2            survival_2.37-7          tcltk_3.0.2
> [82] tools_3.0.2              vsn_3.30.0               xtable_1.7-1
> [85] zlibbioc_1.8.0
>
> Thank you.
>
> Juerg Straubhaar
> University of Massachusetts Medical School
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