[BioC] svg error in arrayQualityMetrics

[Straubhaar, Juerg]

Hi Wolfgang,

My cairo version is 1.12.14 and I didn't like to update to your version since for gentoo linux version 1.12.16 is still unstable.

But I used arrayQualityMetrics devel version and it worked with cairo version 1.12.14.

I apologize for bothering you. I should have thought about  testing the devel package version before using the list.

Thank you.

Juerg
________________________________________
From: Wolfgang Huber [whuber at embl.de]
Sent: Sunday, March 09, 2014 6:18 PM
To: Straubhaar, Juerg
Cc: bioconductor at r-project.org
Subject: Re: [BioC] svg error in arrayQualityMetrics

Dear Juerg

what do you get from
$ pkg-config --modversion cairo

E.g. on my system I get 1.12.16.

Also, please try with the current devel version of the package: http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics.html

Only if all that fails it seems worthwhile to descend into code debugging.

        Kind regards
                Wolfgang


Il giorno 07 Mar 2014, alle ore 19:17, Straubhaar, Juerg <Juerg.Straubhaar at umassmed.edu> ha scritto:

> 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
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor