I have been using cummeRbund for awhile now with relatively no issue but recently I have encountered the following error when trying to do differential expression analysis on an rnaseq experiment:

> cuffdata<-readCufflinks()
Creating database E:/VB-ubuntu/UbuntuShared/Alexproject/cuffdiffalex/cuffData.db
Reading Run Info File E:/VB-ubuntu/UbuntuShared/Alexproject/cuffdiffalex/run.info
Writing runInfo Table
Reading Read Group Info  E:/VB-ubuntu/UbuntuShared/Alexproject/cuffdiffalex/read_groups.info
Writing replicates Table
Reading Var Model Info  E:/VB-ubuntu/UbuntuShared/Alexproject/cuffdiffalex/var_model.info
Writing varModel Table
Reading E:/VB-ubuntu/UbuntuShared/Alexproject/cuffdiffalex/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)

This is my session info:

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] cummeRbund_2.18.0    Gviz_1.20.0         
 [3] rtracklayer_1.36.4   GenomicRanges_1.28.4
 [5] GenomeInfoDb_1.12.2  IRanges_2.10.2      
 [7] S4Vectors_0.14.3     fastcluster_1.1.22  
 [9] reshape2_1.4.2       ggplot2_2.2.1       
[11] RSQLite_2.0          BiocGenerics_0.22.0 

loaded via a namespace (and not attached):
 [1] httr_1.2.1                   
 [2] Biobase_2.36.2               
 [3] AnnotationHub_2.8.2          
 [4] bit64_0.9-7                  
 [5] splines_3.4.1                
 [6] shiny_1.0.3                  
 [7] Formula_1.2-2                
 [8] interactiveDisplayBase_1.14.0
 [9] latticeExtra_0.6-28          
[10] blob_1.1.0                   
[11] BSgenome_1.44.0              
[12] GenomeInfoDbData_0.99.0      
[13] Rsamtools_1.28.0             
[14] yaml_2.1.14                  
[15] backports_1.1.0              
[16] lattice_0.20-35              
[17] biovizBase_1.24.0            
[18] digest_0.6.12                
[19] RColorBrewer_1.1-2           
[20] XVector_0.16.0               
[21] checkmate_1.8.3              
[22] colorspace_1.3-2             
[23] httpuv_1.3.5                 
[24] htmltools_0.3.6              
[25] Matrix_1.2-10                
[26] plyr_1.8.4                   
[27] pkgconfig_2.0.1              
[28] XML_3.98-1.9                 
[29] biomaRt_2.32.1               
[30] zlibbioc_1.22.0              
[31] xtable_1.8-2                 
[32] scales_0.4.1                 
[33] BiocParallel_1.10.1          
[34] htmlTable_1.9                
[35] tibble_1.3.3                 
[36] AnnotationFilter_1.0.0       
[37] SummarizedExperiment_1.6.3   
[38] GenomicFeatures_1.28.4       
[39] nnet_7.3-12                  
[40] lazyeval_0.2.0               
[41] mime_0.5                     
[42] survival_2.41-3              
[43] magrittr_1.5                 
[44] memoise_1.1.0                
[45] foreign_0.8-69               
[46] BiocInstaller_1.26.0         
[47] tools_3.4.1                  
[48] data.table_1.10.4            
[49] matrixStats_0.52.2           
[50] stringr_1.2.0                
[51] munsell_0.4.3                
[52] cluster_2.0.6                
[53] DelayedArray_0.2.7           
[54] AnnotationDbi_1.38.1         
[55] ensembldb_2.0.3              
[56] Biostrings_2.44.1            
[57] compiler_3.4.1               
[58] rlang_0.1.1                  
[59] RCurl_1.95-4.8               
[60] dichromat_2.0-0              
[61] VariantAnnotation_1.22.3     
[62] htmlwidgets_0.9              
[63] bitops_1.0-6                 
[64] base64enc_0.1-3              
[65] gtable_0.2.0                 
[66] curl_2.7                     
[67] DBI_0.7                      
[68] R6_2.2.2                     
[69] GenomicAlignments_1.12.1     
[70] gridExtra_2.2.1              
[71] knitr_1.16                   
[72] bit_1.1-12                   
[73] Hmisc_4.0-3                  
[74] ProtGenerics_1.8.0           
[75] stringi_1.1.5                
[76] Rcpp_0.12.12                 
[77] rpart_4.1-11                 
[78] acepack_1.4.1 

I know that others have encountered this error as well and that it is likely a bug but are there any fixes available?