Hi, I just noticed that the axis labels, title and legend text have gone missing on some of the plots in the quality report. In fact I am not sure which upgrade caused the problem. More specifically, it is the three interactive plots that are missing text labels. The interactive mouse-over text works fine, it is only the static text that is missing from: Figure 3: Principal Component Analysis. Figure 6: Density plots. Figure 12: RNA digestion plot. Is anyone else having this problem? Or am I missing some dependencies in my installation (see below)? I am using the most recent development version of arrayQualityMetrics. Best, Daniel > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_3.13.5 loaded via a namespace (and not attached): [1] affy_1.34.0 affyio_1.24.0 affyPLM_1.32.0 [4] annotate_1.34.0 AnnotationDbi_1.18.1 beadarray_2.6.0 [7] BeadDataPackR_1.8.0 Biobase_2.16.0 BiocGenerics_0.2.0 [10] BiocInstaller_1.4.7 Biostrings_2.24.1 Cairo_1.5-1 [13] cluster_1.14.2 colorspace_1.1-1 DBI_0.2-5 [16] genefilter_1.38.0 grid_2.15.1 Hmisc_3.9-3 [19] hwriter_1.3 IRanges_1.14.3 lattice_0.20-6 [22] latticeExtra_0.6-19 limma_3.12.1 plyr_1.7.1 [25] preprocessCore_1.18.0 RColorBrewer_1.0-5 reshape2_1.2.1 [28] RSQLite_0.11.1 setRNG_2011.11-2 splines_2.15.1 [31] stats4_2.15.1 stringr_0.6 survival_2.36-14 [34] SVGAnnotation_0.9-0 vsn_3.24.0 XML_3.9-4 [37] xtable_1.7-0 zlibbioc_1.2.0

Dear Daniel thanks. I have not seen this type of problem before and am not sure exactly what your problem is. Can you send me (perhaps offline) the script that you use to produce the report, the report itself (tar- zipped directory), and ideally the data set (you can anonymize the samples / genes). Also, the output of pkg-config --modversion cairo Best wishes Wolfgang Jul/4/12 1:56 PM, Daniel Aaen Hansen scripsit:: > Hi, > > I just noticed that the axis labels, title and legend text have gone missing on some of the plots in the quality report. In fact I am not sure which upgrade caused the problem. More specifically, it is the three interactive plots that are missing text labels. The interactive mouse-over text works fine, it is only the static text that is missing from: > > Figure 3: Principal Component Analysis. > Figure 6: Density plots. > Figure 12: RNA digestion plot. > > Is anyone else having this problem? Or am I missing some dependencies in my installation (see below)? I am using the most recent development version of arrayQualityMetrics. > > Best, > Daniel > > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] arrayQualityMetrics_3.13.5 > > loaded via a namespace (and not attached): > [1] affy_1.34.0 affyio_1.24.0 affyPLM_1.32.0 > [4] annotate_1.34.0 AnnotationDbi_1.18.1 beadarray_2.6.0 > [7] BeadDataPackR_1.8.0 Biobase_2.16.0 BiocGenerics_0.2.0 > [10] BiocInstaller_1.4.7 Biostrings_2.24.1 Cairo_1.5-1 > [13] cluster_1.14.2 colorspace_1.1-1 DBI_0.2-5 > [16] genefilter_1.38.0 grid_2.15.1 Hmisc_3.9-3 > [19] hwriter_1.3 IRanges_1.14.3 lattice_0.20-6 > [22] latticeExtra_0.6-19 limma_3.12.1 plyr_1.7.1 > [25] preprocessCore_1.18.0 RColorBrewer_1.0-5 reshape2_1.2.1 > [28] RSQLite_0.11.1 setRNG_2011.11-2 splines_2.15.1 > [31] stats4_2.15.1 stringr_0.6 survival_2.36-14 > [34] SVGAnnotation_0.9-0 vsn_3.24.0 XML_3.9-4 > [37] xtable_1.7-0 zlibbioc_1.2.0 > > _______________________________________________ > 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 > -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber