[BioC] svg error in arrayQualityMetrics

[Wolfgang Huber]

Il giorno 10 Mar 2014, alle ore 14:59, Straubhaar, Juerg <Juerg.Straubhaar at umassmed.edu> ha scritto:

> 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.
> 


Hi Juerg
no problem. These things are complex.

Anyway, as a general principle, it is true, before reporting a bug or a problem, it is good to try with the latest version in devel.
For many we things we find, we find that others have found them before.

	Wolfgang



> 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
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