While generation of quality metrics using ChIPQC for files without peak data has been resolved (ChIPQC without peak calls), I am unable to save HTML reports for those ChIPQC runs.

ChIPQCreport fails, apparently due to attempting to invoke plotCorHeatmap, despite the absence of peaks:

> experiment
Samples: 2 : ENCFF863PSQ ENCFF631ENA 
            Tissue Factor     Control Replicate
ENCFF863PSQ  DOHH2   CTCF ENCFF631ENA         1
               Reads Map% Filt% Dup% ReadL FragL RelCC   SSD RiP%
ENCFF863PSQ 12409070  100     0    0    36   252 5.230 0.176   NA
ENCFF631ENA 23751742  100     0    0    36   229 0.973 0.112   NA

> ChIPQCreport(experiment, facet=F)
Saving 7 x 7 in image
Saving 7 x 7 in image
Error in plotCorHeatmap(object, attributes = c(facetBy, colourBy)) : 
  No peaks to plot.
In addition: Warning messages:
1: In grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  X11 used font size 34 when 45 was requested
2: In grid.Call.graphics(L_rect, x$x, x$y, x$width, x$height, resolveHJust(x$just,  :
  semi-transparency is not supported on this device: reported only once per page
3: In grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  X11 used font size 34 when 45 was requested
4: In grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  X11 used font size 34 when 83 was requested
5: In grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  X11 used font size 34 when 66 was requested

> traceback()
5: stop("No peaks to plot.")
4: plotCorHeatmap(object, attributes = c(facetBy, colourBy))
3: plotCorHeatmap(object, attributes = c(facetBy, colourBy))
2: ChIPQCreport(experiment, facet = F)
1: ChIPQCreport(experiment, facet = F)

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)

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=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] ChIPQC_1.8.7               DiffBind_2.0.2            
 [3] SummarizedExperiment_1.2.3 Biobase_2.32.0            
 [5] GenomicRanges_1.24.2       GenomeInfoDb_1.8.1        
 [7] IRanges_2.6.1              S4Vectors_0.10.1          
 [9] BiocGenerics_0.18.0        ggplot2_2.1.0             

loaded via a namespace (and not attached):
 [1] edgeR_3.14.0                             
 [2] splines_3.3.0                            
 [3] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
 [4] TxDb.Mmusculus.UCSC.mm10.knownGene_3.2.2 
 [5] gtools_3.5.0                             
 [6] assertthat_0.1                           
 [7] latticeExtra_0.6-28                      
 [8] amap_0.8-14                              
 [9] RBGL_1.48.1                              
[10] Rsamtools_1.24.0                         
[11] Category_2.38.0                          
[12] RSQLite_1.0.0                            
[13] backports_1.0.2                          
[14] lattice_0.20-33                          
[15] limma_3.28.10                            
[16] digest_0.6.10                            
[17] RColorBrewer_1.1-2                       
[18] XVector_0.12.0                           
[19] checkmate_1.8.0                          
[20] colorspace_1.2-6                         
[21] Matrix_1.2-6                             
[22] plyr_1.8.4                               
[23] GSEABase_1.34.0                          
[24] chipseq_1.22.0                           
[25] TxDb.Hsapiens.UCSC.hg38.knownGene_3.1.3  
[26] XML_3.98-1.4                             
[27] pheatmap_1.0.8                           
[28] ShortRead_1.30.0                         
[29] biomaRt_2.28.0                           
[30] genefilter_1.54.2                        
[31] zlibbioc_1.18.0                          
[32] xtable_1.8-2                             
[33] GO.db_3.3.0                              
[34] scales_0.4.0                             
[35] brew_1.0-6                               
[36] gdata_2.17.0                             
[37] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
[38] BiocParallel_1.6.2                       
[39] annotate_1.50.0                          
[40] GenomicFeatures_1.24.2                   
[41] survival_2.39-4                          
[42] magrittr_1.5                             
[43] systemPipeR_1.6.2                        
[44] fail_1.3                                 
[45] gplots_3.0.1                             
[46] hwriter_1.3.2                            
[47] GOstats_2.38.0                           
[48] graph_1.50.0                             
[49] tools_3.3.0                              
[50] BBmisc_1.9                               
[51] stringr_1.1.0                            
[52] sendmailR_1.2-1                          
[53] munsell_0.4.3                            
[54] locfit_1.5-9.1                           
[55] AnnotationDbi_1.34.3                     
[56] Biostrings_2.40.2                        
[57] caTools_1.17.1                           
[58] grid_3.3.0                               
[59] RCurl_1.95-4.8                           
[60] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2     
[61] rjson_0.2.15                             
[62] AnnotationForge_1.14.2                   
[63] labeling_0.3                             
[64] bitops_1.0-6                             
[65] base64enc_0.1-3                          
[66] gtable_0.2.0                             
[67] DBI_0.4-1                                
[68] reshape2_1.4.1                           
[69] R6_2.1.3                                 
[70] GenomicAlignments_1.8.3                  
[71] Nozzle.R1_1.1-1                          
[72] dplyr_0.4.3                              
[73] rtracklayer_1.32.1                       
[74] KernSmooth_2.23-15                       
[75] stringi_1.1.1                            
[76] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
[77] BatchJobs_1.6                            
[78] Rcpp_0.12.7                              
[79] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[80] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2