Hi,
I was trying to run the basic functionality of RnBeads. However, no pdfs are produced. Here is the code and warnings/errors:
### run QC
> rnb.run.qc(rnb.set3, report.dir)
.
.
**** Warning: Invalid Page count.
**** Warning: Invalid Page count.
No pages will be processed (FirstPage > LastPage).
**** This file had errors that were repaired or ignored.
**** The file was produced by:
**** >>>> R 3.2.2 <<<<
**** Please notify the author of the software that produced this
**** file that it does not conform to Adobe's published PDF
**** specification.
TableGrob (2 x 1) "arrange": 2 grobs
z cells name grob
1 1 (1-1,1-1) arrange gtable[layout]
2 2 (2-2,1-1) arrange gtable[layout]
**** Warning: Invalid Page count.
**** Warning: Invalid Page count.
No pages will be processed (FirstPage > LastPage).
===================================================
The pdfs are produced (each pdf is 4 kb, so empty) and I can't open them. Perhaps I am missing a required package? The code appears to be nested too deeply (for me!) to try to debug. My info:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11 (El Capitan)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets
[9] methods base
other attached packages:
[1] RnBeads.hg19_1.2.0 hash_2.2.6
[3] org.Mm.eg.db_3.2.3 BiocInstaller_1.20.0
[5] XML_3.98-1.3 reshape_0.8.5
[7] data.table_1.9.6 foreign_0.8-66
[9] preprocessCore_1.32.0 gtools_3.5.0
[11] methylKit_0.9.5 devtools_1.9.1
[13] RnBeads_1.2.0 plyr_1.8.3
[15] methylumi_2.16.0 minfi_1.16.0
[17] bumphunter_1.10.0 locfit_1.5-9.1
[19] iterators_1.0.8 foreach_1.4.3
[21] Biostrings_2.38.0 XVector_0.10.0
[23] SummarizedExperiment_1.0.0 lattice_0.20-33
[25] FDb.InfiniumMethylation.hg19_2.2.0 org.Hs.eg.db_3.2.3
[27] RSQLite_1.0.0 DBI_0.3.1
[29] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.22.0
[31] AnnotationDbi_1.32.0 reshape2_1.4.1
[33] scales_0.3.0 Biobase_2.30.0
[35] illuminaio_0.12.0 matrixStats_0.14.2
[37] limma_3.26.0 gridExtra_2.0.0
[39] gplots_2.17.0 ggplot2_1.0.1
[41] fields_8.3-5 maps_3.0.0-2
[43] spam_1.2-1 ff_2.2-13
[45] bit_1.1-12 cluster_2.0.3
[47] RColorBrewer_1.1-2 MASS_7.3-44
[49] GenomicRanges_1.22.0 GenomeInfoDb_1.6.0
[51] IRanges_2.4.0 S4Vectors_0.8.0
[53] BiocGenerics_0.16.0
loaded via a namespace (and not attached):
[1] nlme_3.1-122 bitops_1.0-6 tools_3.2.2
[4] doRNG_1.6 nor1mix_1.2-1 KernSmooth_2.23-15
[7] colorspace_1.2-6 base64_1.1 chron_2.3-47
[10] pkgmaker_0.22 labeling_0.3 rtracklayer_1.30.0
[13] caTools_1.17.1 genefilter_1.52.0 quadprog_1.5-5
[16] stringr_1.0.0 digest_0.6.8 Rsamtools_1.22.0
[19] siggenes_1.44.0 GEOquery_2.36.0 mclust_5.0.2
[22] BiocParallel_1.4.0 RCurl_1.95-4.7 magrittr_1.5
[25] futile.logger_1.4.1 Rcpp_0.12.1 munsell_0.4.2
[28] proto_0.3-10 stringi_0.5-5 zlibbioc_1.16.0
[31] gdata_2.17.0 splines_3.2.2 multtest_2.26.0
[34] annotate_1.48.0 beanplot_1.2 igraph_1.0.1
[37] rngtools_1.2.4 codetools_0.2-14 biomaRt_2.26.0
[40] mixOmics_5.1.2 futile.options_1.0.0 lambda.r_1.1.7
[43] gtable_0.1.2 xtable_1.7-4 survival_2.38-3
[46] pheatmap_1.0.7 memoise_0.2.1 ellipse_0.3-8
[49] GenomicAlignments_1.6.0 registry_0.3 rgl_0.95.1367
