Error when using the force=TRUE option in read.metharray.sheet

Hi there and thanks for a great package. I'm trying to read some EPIC array data and it looks like my arrays have different numbers of probes:

targets <- read.metharray.sheet(data_dir)
RGset <- read.metharray.exp(targets = targets, verbose = TRUE)

[read.metharray] Creating data matrices ... 
Error in read.metharray(files, extended = extended, verbose = verbose,  : 
  [read.metharray] Trying to parse IDAT files with different array size but seemingly all of the same type.
  You can force this by 'force=TRUE', see the man page ?read.metharray

So I tried it with the force=TRUE option and a get an error:

targets <- read.metharray.sheet(data_dir)
RGset <- read.metharray.exp(targets = targets, verbose = TRUE, force=TRUE)

[read.metharray] Instantiating final object ...
Error in `sampleNames<-`(`*tmp*`, value = c("1600101", "1600111", "1600115",  :
  number of new names (1051943) should equal number of rows in AnnotatedDataFrame (1051539)
Calls: read.metharray.exp ... featureNames<- -> featureNames<- -> sampleNames<- -> sampleNames<-
Execution halted

Session info:


R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.6 (unknown)

locale:
[1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8

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

other attached packages:
 [1] ChAMP_2.6.4                               
 [2] IlluminaHumanMethylationEPICmanifest_0.3.0
 [3] Illumina450ProbeVariants.db_1.10.0        
 [4] DMRcate_1.10.10                           
 [5] DMRcatedata_1.10.1                        
 [6] DSS_2.14.0                                
 [7] bsseq_1.10.0                              
 [8] FEM_3.2.0                                 
 [9] graph_1.52.0                              
[10] org.Hs.eg.db_3.4.0                        
[11] impute_1.48.0                             
[12] igraph_1.2.2                              
[13] corrplot_0.84                             
[14] marray_1.52.0                             
[15] limma_3.30.13                             
[16] Matrix_1.2-6                              
[17] AnnotationDbi_1.36.2                      
[18] ChAMPdata_2.6.0                           
[19] minfi_1.20.2                              
[20] bumphunter_1.14.0                         
[21] locfit_1.5-9.1                            
[22] iterators_1.0.10                          
[23] foreach_1.4.4                             
[24] Biostrings_2.42.1                         
[25] XVector_0.14.1                            
[26] SummarizedExperiment_1.4.0                
[27] GenomicRanges_1.26.4                      
[28] GenomeInfoDb_1.10.3                       
[29] IRanges_2.8.2                             
[30] S4Vectors_0.12.2                          
[31] Biobase_2.34.0                            
[32] BiocGenerics_0.20.0                       

loaded via a namespace (and not attached):
  [1] R.utils_2.6.0                                      
  [2] tidyselect_0.2.4                                   
  [3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
  [4] RSQLite_2.1.1                                      
  [5] htmlwidgets_1.2                                    
  [6] trimcluster_0.1-2.1                                
  [7] grid_3.3.0                                         
  [8] BiocParallel_1.8.2                                 
  [9] munsell_0.4.3                                      
 [10] codetools_0.2-15                                   
 [11] preprocessCore_1.36.0                              
 [12] statmod_1.4.30                                     
 [13] withr_2.1.2                                        
 [14] colorspace_1.2-6                                   
 [15] fastICA_1.2-1                                      
 [16] BiocInstaller_1.24.0                               
 [17] knitr_1.20                                         
 [18] rstudioapi_0.7                                     
 [19] robustbase_0.93-2                                  
 [20] JADE_2.0-1                                         
 [21] isva_1.9                                           
 [22] bit64_0.9-7                                        
 [23] biovizBase_1.22.0                                  
 [24] diptest_0.75-7                                     
 [25] R6_2.2.2                                           
 [26] doParallel_1.0.11                                  
 [27] illuminaio_0.16.0                                  
 [28] clue_0.3-55                                        
 [29] flexmix_2.3-14                                     
 [30] bitops_1.0-6                                       
 [31] reshape_0.8.7                                      
 [32] assertthat_0.2.0                                   
 [33] promises_1.0.1                                     
 [34] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 
 [35] scales_0.5.0                                       
 [36] nnet_7.3-12                                        
 [37] gtable_0.2.0                                       
 [38] methylumi_2.20.0                                   
 [39] sva_3.22.0                                         
 [40] ensembldb_1.6.2                                    
 [41] rlang_0.2.1                                        
 [42] genefilter_1.56.0                                  
 [43] rtracklayer_1.34.2                                 
 [44] lazyeval_0.2.1                                     
 [45] acepack_1.4.1                                      
 [46] GEOquery_2.40.0                                    
 [47] dichromat_2.0-0                                    
 [48] checkmate_1.8.5                                    
 [49] yaml_2.2.0                                         
 [50] reshape2_1.4.1                                     
 [51] GenomicFeatures_1.26.4                             
 [52] backports_1.1.2                                    
 [53] httpuv_1.4.5                                       
 [54] qvalue_2.6.0                                       
 [55] Hmisc_4.1-1                                        
 [56] tools_3.3.0                                        
 [57] nor1mix_1.2-3                                      
 [58] ggplot2_3.0.0                                      
 [59] RColorBrewer_1.1-2                                 
 [60] DNAcopy_1.48.0                                     
 [61] siggenes_1.48.0                                    
 [62] Rcpp_0.12.18                                       
 [63] plyr_1.8.3                                         
 [64] base64enc_0.1-3                                    
 [65] zlibbioc_1.20.0                                    
 [66] purrr_0.2.5                                        
 [67] RCurl_1.95-4.11                                    
 [68] BiasedUrn_1.07                                     
 [69] rpart_4.1-10                                       
 [70] openssl_1.0.2                                      
 [71] viridis_0.5.1                                      
 [72] cluster_2.0.4                                      
 [73] magrittr_1.5                                       
 [74] data.table_1.11.4                                  
 [75] goseq_1.26.0                                       
 [76] mvtnorm_1.0-8                                      
 [77] whisker_0.3-2                                      
 [78] wateRmelon_1.18.0                                  
 [79] matrixStats_0.54.0                                 
 [80] missMethyl_1.8.0                                   
 [81] RPMM_1.25                                          
 [82] mime_0.5                                           
 [83] xtable_1.8-2                                       
 [84] XML_3.98-1.13                                      
 [85] mclust_5.4.1                                       
 [86] gridExtra_2.3                                      
 [87] biomaRt_2.30.0                                     
 [88] tibble_1.4.2                                       
 [89] crayon_1.3.4                                       
 [90] R.oo_1.22.0                                        
 [91] htmltools_0.3.6                                    
 [92] mgcv_1.8-12                                        
 [93] later_0.7.3                                        
 [94] Formula_1.2-3                                      
 [95] tidyr_0.8.1                                        
 [96] DBI_1.0.0                                          
 [97] geneLenDataBase_1.10.0                             
 [98] fpc_2.1-11.1                                       
 [99] MASS_7.3-45                                        
[100] permute_0.9-4                                      
[101] quadprog_1.5-5                                     
[102] R.methodsS3_1.7.1                                  
[103] Gviz_1.18.2                                        
[104] bindr_0.1.1                                        
[105] pkgconfig_2.0.1                                    
[106] RefFreeEWAS_2.1                                    
[107] GenomicAlignments_1.10.1                           
[108] registry_0.5                                       
[109] IlluminaHumanMethylation450kmanifest_0.4.0         
[110] foreign_0.8-66                                     
[111] plotly_4.8.0                                       
[112] annotate_1.52.1                                    
[113] rngtools_1.3.1                                     
[114] pkgmaker_0.27                                      
[115] multtest_2.30.0                                    
[116] beanplot_1.2                                       
[117] ruv_0.9.7                                          
[118] bibtex_0.4.2                                       
[119] doRNG_1.7.1                                        
[120] stringr_1.0.0                                      
[121] VariantAnnotation_1.20.3                           
[122] digest_0.6.9                                       
[123] base64_2.0                                         
[124] htmlTable_1.12                                     
[125] dendextend_1.8.0                                   
[126] kernlab_0.9-26                                     
[127] modeltools_0.2-22                                  
[128] shiny_1.1.0                                        
[129] Rsamtools_1.26.2                                   
[130] gtools_3.5.0                                       
[131] nlme_3.1-127                                       
[132] jsonlite_1.5                                       
[133] bindrcpp_0.2.2                                     
[134] viridisLite_0.3.0                                  
[135] BSgenome_1.42.0                                    
[136] pillar_1.3.0                                       
[137] lattice_0.20-33                                    
[138] DEoptimR_1.0-8                                     
[139] httr_1.3.1                                         
[140] survival_2.42-6                                    
[141] GO.db_3.4.0                                        
[142] interactiveDisplayBase_1.12.0                      
[143] glue_1.3.0                                         
[144] prabclus_2.2-6                                     
[145] shinythemes_1.1.1                                  
[146] bit_1.1-14                                         
[147] class_7.3-14                                       
[148] stringi_1.1.1                                      
[149] blob_1.1.1                                         
[150] AnnotationHub_2.6.5                                
[151] latticeExtra_0.6-28                                
[152] memoise_1.1.0                                      
[153] dplyr_0.7.6

hansenlab / minfi

Error when using the force=TRUE option in read.metharray.sheet #173