RnBeads - doesn't produce pdfs
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Entering edit mode
Brian Smith ▴ 120
@brian-smith-6197
Last seen 2.0 years ago
United States

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 

 

rnbeads illumina450k • 1.4k views
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1
Entering edit mode
pavlo.lutsik ▴ 10
@pavlolutsik-9032
Last seen 6.9 years ago
Germany

This error is due to changes in some of the RnBeads dependencies. Specifically, the print() method does not triger plotting of the frame grob anymore, causing the plot generation to fail for some of the QC plots. The fixes will be a part of the official RnBeads release in the near future. In the meanwhile you can workaround this issue by overriding the default printing method for the gtable objects. Before running RnBeads call:

print.gtable<-grid.draw

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